Re: [gmx-users] LINCS Constraints - all-bonds or h-bonds?
I often use 4 fs with all-bonds and virtual sites, especially if lacking sampling is a greater source of error than the kinetic energy being slightly off. Erik On 15 Aug 2013, at 20:58, Michael Shirts mrshi...@gmail.com wrote: I don't go beyond 2 fs with either all- bonds or h-bonds. Things like kinetic energy start being subtly off. H-bonds has less chance of failing with large numbers of constraints- less iteration required, especially if bond system cross parallelization boundaries. If your molecules are 10 atoms, it probably doesn't matter either way. Sent from my iPhone On Aug 15, 2013, at 9:11, Barnett, James W. jbarn...@tulane.edu wrote: Searching through this mailing list it seems like some have stated that with a 2 fs timestep (dt=0.002), constraints=h-bonds is fine in general. The questions I have are: 1) What are some personal opinions on when it is ok to switch to h-bonds from all-bonds for LINCS constraints? Is 2 fs and h-bonds a general practice? 2) Also, if typically 2 fs and h-bonds are ok, what time-step do users (or you personally) generally go to with all-bonds? I am speaking generally here of course. Thanks for your responses. -- Wes Barnett | jbarn...@tulane.edu -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] meaning of results of g_hbond -ac
* Time
* Ac(hbond) with correction for the fact that a finite system is being
simulated.
* Ac(hbond) without correction
* Cross correlation between hbonds and contacts (see the papers by
LuzarChandler and van der Spoel that are mentioned in the stdout from g_hbond)
* Derivative of second column.
On 18 Jul 2013, at 04:51, Wu Chaofu xiaowu...@gmail.com wrote:
Dear gmxers,
By running the command g_hbond -ac, a resulting .xvg file is generated,
which is attached below. In that file, there are five columns. I guess
that, the first column is time, the second the HB autocorrelation function.
But what are the other columns denoted by s1, s2, s3? Thanks a lot for any
reply.
Yours sincerely,
Chaofu Wu
# This file was created Wed Jul 17 09:49:34 2013
# by the following command:
# g_hbond -f iconf.xtc -s conf.tpr -n -ac ihbac2.xvg
#
# g_hbond is part of G R O M A C S:
#
# GROtesk MACabre and Sinister
#
@title Hydrogen Bond Autocorrelation
@xaxis label Time (ps)
@yaxis label C(t)
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend Ac\sfin sys\v{}\z{}(t)
@ s1 legend Ac(t)
@ s2 legend Cc\scontact,hb\v{}\z{}(t)
@ s3 legend -dAc\sfs\v{}\z{}/dt
0 1 1 -5.79228e-110.902311
1 0.09955770.1001860.1345570.455234
2 0.0895326 0.09016760.126435 0.00815676
3 0.0832442 0.08388360.123311 0.00541426
4 0.0787041 0.07934660.117936 0.00376486
5 0.0757145 0.07635910.116489 0.00198866
6 0.0747267 0.07537210.112655 0.00177937
7 0.0721557 0.07280290.109565 0.00255146
8 0.0696238 0.07027270.107288 0.00241577
9 0.0673242 0.06797470.106287 0.00157028
10 0.0664832 0.06713430.104746 0.0014926
110.064339 0.06499160.101947 0.00148105
12 0.0635211 0.0641743 0.0991141 0.00131835
13 0.0617023 0.06235670.101322 0.00147757
140.060566 0.0612212 0.0965892 0.000719808
.
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Re: [gmx-users] UMBRELLA SAMPLING
It's just the xvv file. g_wham uses the letter 'z' to denote the reaction coordinate. Erik On 2 Jul 2013, at 11:32, battis...@libero.it wrote: Dear users and experts I'm doing an umbrella-samplig calculation to obtain the PMF when two structure (A and B) are at various X distances. I setted my md-umbrella.mdp file as in follows: ; COM PULLING ; Pull type: no, umbrella, constraint or constant_force pull = umbrella pull_geometry= distance pull_dim = Y N N pull_start = yes pull_nstxout = 1000 pull_nstfout = 1000 ; Number of pull groups pull_ngroups = 1 pull_group0 = A pull_group1 = B pull_init1 = 0 pull_rate1 = 0.0 pull_k1 = 1000 pull_kB1 = 1000 but when I run the program g_wham: g_wham -it tpr-files.dat -if pullf-files.dat -o profile.xvg -hist histo.xvg the profile I obtain is respect to the z coordinate (PMF as a function of z). My question is: is this only a problem of xvg text, or the PMF is effectively calculated with respect to the z variable, although I selected pull_dim = Y N N? Thank you very much Anna -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] autocorrelation output g_hbond
Hi, Yes, the forward and backward rate constants are for hydrogen-bond breaking and reforming. You seem to have too poor statistics to draw conclusions about the backward rate, however. You probably need to simulate longer. Erik On 15 Jun 2013, at 00:38, learnmd joinforfun8...@gmail.com wrote: Hi, I have run a 5 ns simulation with a small protein in water [SPCE]. I am interested in the rate of breakage (sense of how quickly / slowly hbonds are broken and formed) of hbonds between protein and solvent. I ran g_hbond -ac for the trajectory and received the following output: Normalization for c(t) = 0.0204961 for gh(t) = 4.55478e-07 Hydrogen bond thermodynamics at T = 298.15 K Fitting parameters chi^2 = 0.0335188 Q = 0 -- Type Rate (1/ps) Time (ps) DG (kJ/mol) Chi^2 Forward 0.022 46.303 14.035 0.0335188 Backward -0.080-12.447-666.000 One-way 0.068 14.603 11.175 Integral0.020 48.944 14.173 Relaxation 0.052 19.211 11.854 My question is that the 46 ps that is shown for forward can be interpreted in the sense that I have described above? Or am I missing the point, completely. I am grateful for any pointers. Thanks -- View this message in context: http://gromacs.5086.x6.nabble.com/autocorrelation-output-g-hbond-tp5009171.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] autocorrelation output g_hbond
…or the hydrogen-bond kinetics of your system may not fit the Luzar-Chandler model for whatever reason. Erik On 17 Jun 2013, at 13:22, Erik Marklund er...@xray.bmc.uu.se wrote: Hi, Yes, the forward and backward rate constants are for hydrogen-bond breaking and reforming. You seem to have too poor statistics to draw conclusions about the backward rate, however. You probably need to simulate longer. Erik On 15 Jun 2013, at 00:38, learnmd joinforfun8...@gmail.com wrote: Hi, I have run a 5 ns simulation with a small protein in water [SPCE]. I am interested in the rate of breakage (sense of how quickly / slowly hbonds are broken and formed) of hbonds between protein and solvent. I ran g_hbond -ac for the trajectory and received the following output: Normalization for c(t) = 0.0204961 for gh(t) = 4.55478e-07 Hydrogen bond thermodynamics at T = 298.15 K Fitting parameters chi^2 = 0.0335188 Q = 0 -- Type Rate (1/ps) Time (ps) DG (kJ/mol) Chi^2 Forward 0.022 46.303 14.035 0.0335188 Backward -0.080-12.447-666.000 One-way 0.068 14.603 11.175 Integral0.020 48.944 14.173 Relaxation 0.052 19.211 11.854 My question is that the 46 ps that is shown for forward can be interpreted in the sense that I have described above? Or am I missing the point, completely. I am grateful for any pointers. Thanks -- View this message in context: http://gromacs.5086.x6.nabble.com/autocorrelation-output-g-hbond-tp5009171.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] dssp works fine, but do_dssp gives fatal error
Hi, Search the mailing list. This problem and its solution has been repeatedly discussed. Erik On 12 Jun 2013, at 10:31, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: Dear all, I installed dssp (Version 2.0.4) and it works perfect on a .pdb file. I am trying to use it for do_dssp command but get the following error each time: Fatal error: Failed to execute command: /usr/local/bin/dssp -na ddtmi68v ddwLuK68 /dev/null 2 /dev/null Is there any way to rectify it? Thanks. Nikunj -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] dssp works fine, but do_dssp gives fatal error
Search again. The syntax for invoking dssp changed at some point and it took a while before do_dssp adapted to that. If your do_dssp is lacking the -ver option then I'm quite confident that it uses the old syntax, which doesn't work with the newer versions (v. 2.0+ I think) of dssp. Erik On 12 Jun 2013, at 11:17, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: Yes I did searched. But for most people, there were issues regarding the path or wrong DSSP. DSSP runs for me, but do_dssp does not. On Wed, Jun 12, 2013 at 2:25 PM, Erik Marklund er...@xray.bmc.uu.se wrote: Hi, Search the mailing list. This problem and its solution has been repeatedly discussed. Erik On 12 Jun 2013, at 10:31, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: Dear all, I installed dssp (Version 2.0.4) and it works perfect on a .pdb file. I am trying to use it for do_dssp command but get the following error each time: Fatal error: Failed to execute command: /usr/local/bin/dssp -na ddtmi68v ddwLuK68 /dev/null 2 /dev/null Is there any way to rectify it? Thanks. Nikunj -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] dssp works fine, but do_dssp gives fatal error
You have (at least) two easy options. 1) Install old_dssp that is available through the dssp web page. 2) Install a newer version of gromacs than you have at the moment. What version do you currently use? Erik On 12 Jun 2013, at 12:56, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: Yes I checked. do_dssp has no -ver option. I also found out this link https://gerrit.gromacs.org/#/c/687/ but dont know how to install/use it. Or maybe I can install DsspOld and see? On Wed, Jun 12, 2013 at 4:15 PM, Erik Marklund er...@xray.bmc.uu.se wrote: Search again. The syntax for invoking dssp changed at some point and it took a while before do_dssp adapted to that. If your do_dssp is lacking the -ver option then I'm quite confident that it uses the old syntax, which doesn't work with the newer versions (v. 2.0+ I think) of dssp. Erik On 12 Jun 2013, at 11:17, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: Yes I did searched. But for most people, there were issues regarding the path or wrong DSSP. DSSP runs for me, but do_dssp does not. On Wed, Jun 12, 2013 at 2:25 PM, Erik Marklund er...@xray.bmc.uu.se wrote: Hi, Search the mailing list. This problem and its solution has been repeatedly discussed. Erik On 12 Jun 2013, at 10:31, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: Dear all, I installed dssp (Version 2.0.4) and it works perfect on a .pdb file. I am trying to use it for do_dssp command but get the following error each time: Fatal error: Failed to execute command: /usr/local/bin/dssp -na ddtmi68v ddwLuK68 /dev/null 2 /dev/null Is there any way to rectify it? Thanks. Nikunj -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] segemntation fault after run do_dssp
HI, What version of gromacs is this? DSSP changed its syntax a while back and we had to adjust do_dssp accordingly. You may have a mismatch between gromacs and dssp versions. Erik On 7 Jun 2013, at 08:42, Nur Syafiqah Abdul Ghani pqah...@gmail.com wrote: Hi All, I already done the MD production so I want to analyse the helical structure of my protein by using do_dssp program.The command is like below : do_dssp -s md_water50.tpr -f md_water50.trr -n mainchain.ndx -sc dssp_scount.xvg -a dssp_area.xvg -ta dssp_totarea.xvg -aa dssp_averarea.xvg but after i run the command the result show like : Reading file md_water50.tpr, VERSION 4.5.5 (double precision) Reading file md_water50.tpr, VERSION 4.5.5 (double precision) Segmentation fault (core dumped) I already install the dssp program from ftp://ftp.cmbi.ru.nl/pub/software/dssp/ and follow the instruction as shown there but it seems that nothing happened..I already gedit the .bashrc for dssp. -- Best Regards, Nur Syafiqah Abdul Ghani, Theoretical and Computational Chemistry Laboratory, Department of Chemistry, Faculty of Science, Universiti Putra Malaysia, 43400 Serdang, Selangor. alternative email : syafiqahabdulgh...@gmail.com @ gs33...@mutiara.upm.edu.my -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] segemntation fault after run do_dssp
Hi, It may very well be. Here's the red mine issue http://redmine.gromacs.org/issues/891. If there's a -ver option for do_dssp then it's capable of the new syntax. If not then it assumes the old syntax. If you can't install a newer version of gromacs there is the option to install old_dssp which is available through the dssp webpage. Erik On 7 Jun 2013, at 10:20, shika pqah...@gmail.com wrote: Hi Eric, I'm using gromacs 4.5.5. Is it the version is different for dssp? Thanks On Fri, Jun 7, 2013 at 3:41 AM, Erik Marklund [via GROMACS] ml-node+s5086n5008885...@n6.nabble.com wrote: HI, What version of gromacs is this? DSSP changed its syntax a while back and we had to adjust do_dssp accordingly. You may have a mismatch between gromacs and dssp versions. Erik On 7 Jun 2013, at 08:42, Nur Syafiqah Abdul Ghani [hidden email] wrote: Hi All, I already done the MD production so I want to analyse the helical structure of my protein by using do_dssp program.The command is like below : do_dssp -s md_water50.tpr -f md_water50.trr -n mainchain.ndx -sc dssp_scount.xvg -a dssp_area.xvg -ta dssp_totarea.xvg -aa dssp_averarea.xvg but after i run the command the result show like : Reading file md_water50.tpr, VERSION 4.5.5 (double precision) Reading file md_water50.tpr, VERSION 4.5.5 (double precision) Segmentation fault (core dumped) I already install the dssp program from ftp://ftp.cmbi.ru.nl/pub/software/dssp/ and follow the instruction as shown there but it seems that nothing happened..I already gedit the .bashrc for dssp. -- Best Regards, Nur Syafiqah Abdul Ghani, Theoretical and Computational Chemistry Laboratory, Department of Chemistry, Faculty of Science, Universiti Putra Malaysia, 43400 Serdang, Selangor. alternative email : [hidden email] @ [hidden email] -- gmx-users mailing list[hidden email] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [hidden email]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list[hidden email] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [hidden email]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists If you reply to this email, your message will be added to the discussion below: http://gromacs.5086.x6.nabble.com/segemntation-fault-after-run-do-dssp-tp5008883p5008885.html To start a new topic under GROMACS Users Forum, email ml-node+s5086n4370410...@n6.nabble.com To unsubscribe from GROMACS, click here. NAML -- Best Regards, Nur Syafiqah Abdul Ghani, Theoretical and Computational Chemistry Laboratory, Department of Chemistry, Faculty of Science, Universiti Putra Malaysia, 43400 Serdang, Selangor. alternative email : syafiqahabdulgh...@gmail.com @ gs33...@mutiara.upm.edu.my -- View this message in context: http://gromacs.5086.x6.nabble.com/segemntation-fault-after-run-do-dssp-tp5008883p5008886.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Vritual Sites and simulation time-step
Hi James, Not related to the integration stability as such, but since the vsites affect the hydrogens by definition perhaps g_hbond can reveal systematic differences between simulations with and without vsites. I believe Feenstra et al did this in the paper describing vsites in the first place. Erik On 3 Jun 2013, at 14:03, James Starlight jmsstarli...@gmail.com wrote: Mark, I've performed 50 ns simulation of water-soluble protein with and without VS. As the consequence I've observed similar behavior of both systems in case of secondfary structure conservation as well as overal degree of conformational dynamics. Also I didnt observed any fluctuation in energy and temperature (using SD as the thermostat and 2ps coupling). Is there any other Gromacs build-in tools on what I should paid more attention during investigation stability of the system with VS ? James 2013/6/2 Mark Abraham mark.j.abra...@gmail.com On Sun, Jun 2, 2013 at 4:56 PM, James Starlight jmsstarli...@gmail.com wrote: Mark, could you also provide me with some examples when usage of VS could give artifacts in simulations ? I don't know of any particular examples. This kind of thing tends to be tested ad hoc - how far can the time step be pushed and still reproduce some relevant observable? See GROMACS generalized Born paper. There is certainly some scope for people to investigate and publish such findings. See, for example, recent publications by Michael Shirts. In particular I'm interesting in usage of VS on hydrogens with membrane proteins. I really don't know anything there :-) I imagine people often use a united-atom lipid for a reason. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] About Checkpoint error in gromacs 4.6
How about running with -noappend? On 1 Jun 2013, at 13:59, vidhya sankar scvsankar_...@yahoo.com wrote: Dear Justin Thank you for your previuos reply I am using gromacs 4.6 AMD 8 core processor When I run restart My run from the Checkpoint file using the following error ./mdrun_d -s CNTPEPRSOLNPT.tpr -cpi CNTPEPRSOLNPT_prev.cpt -v -nt 8 -deffnm CNTPEPRSOLNPT -append The original run wrote a file called 'CNTPEPRSOLNPT.trr' which is larger than 2 GB, but mdrun did not support large file offsets. Can not append. Run mdrun with -noappend How to solve this error? Thnaks In ADVANCE -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] About Compiler Option
gcc is probably still your old version. The new one would probably be called gcc-4.7 or similar. Erik On 30 May 2013, at 15:15, vidhya sankar scvsankar_...@yahoo.com wrote: Dear Justin and other gromacs users , Thank you for your Previous reply I Have AMD Block Edition FX8350 Processor Also I have Ubuntu 10.04 OS Using 8 MPI threads Compiled acceleration: SSE4.1 (Gromacs could use AVX_128_FMA on this machine, which is better) As you mailed me for the aforesaid about performance I want to Ugrade gcc version 4.7.2 already i had version gcc 4.4.3 When I want to Upgrade But Though I give the following Commands add-apt-repository ppa:ubuntu-toolchain-r/test apt-get update apt-get install gcc-4.7 it has not been updated this is confirmed When i check gcc version in terminal -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Have your ever got a real NVE simulation (good energy conservation) in gromacs?
Hi, I have achieved good energy conservation in NVE simulations. This was single proteins in the gas phase, using infinite cut-offs, constraints applied to hydrogens, 0.5 fs or 1.0 fs time steps, double precision and virtual sites if I'm not mistaken. We had problems with energy conservation for the first publication (Patriksson et al 2007, Biochemistry. The methods section states 1.0 fs, but that's a typo for we used 0.5 fs) for 1.0 fs time steps. For a second publication (Marklund et al 2009, PCCP) 1.0 fs worked fine, using a later gromacs version. In the first case we used SHAKE and in the later LINCS I think. Hope that helps Erik On 23 May 2013, at 23:59, cyberjhon cyberj...@hotmail.com wrote: Hi Guys I have been trying by all means to get a real good Energy conservation in NVE simulations using gromacs but it has been almost impossible for me. I have tried many different combinations of Coulomb and VdW parameters and changed the cut off radius and nothing. 1. Have you ever obtained energy conservation in Gromacs? 2. Under what conditions ? for what system? 2. Do you have a set of parameters that works to obtain energy conservation? if you can share with me the mdp file, I will appreciate it. My system is Human Papiloma Virus virus-like particle T=1 inmersed in SPC water. Thanks John Michael Espinsoa Duran -- View this message in context: http://gromacs.5086.x6.nabble.com/Have-your-ever-got-a-real-NVE-simulation-good-energy-conservation-in-gromacs-tp5008501.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_hbond
Hi, Just to clarify: The third column are the number of acceptor-donor pairs that fulfil the distance criterion but not the angle criterion. Erik On 24 May 2013, at 09:06, CHEN Pan evan.pan.c...@gmail.com wrote: Hi Maggin, The middle column is the total number of hydrogen bonds in your system under the definition of the hydrogen bonds criteria you have defined (here you used the default value). The third column is the number of acceptor-donor paris in the system. The first column is the simulation time, your trajectory file are saved every 2 ps right? If you use xmgrace bovin_hnum.xvg, you can easily find what's the meaning of the second and third column. Pan 2013/5/24 maggin maggin.c...@gmail.com # This file was created Fri May 24 13:03:14 2013 # by the following command: # g_hbond -f traj_all_md.trr -s md_0_1_next1.tpr -num bovin_hnum.xvg # # g_hbond is part of G R O M A C S: # # Green Red Orange Magenta Azure Cyan Skyblue # @title Hydrogen Bonds @xaxis label Time (ps) @yaxis label Number @TYPE xy @ view 0.15, 0.15, 0.75, 0.85 @ legend on @ legend box on @ legend loctype view @ legend 0.78, 0.8 @ legend length 2 @ s0 legend Hydrogen bonds @ s1 legend Pairs within 0.35 nm 0 74 517 2 73 515 4 69 515 6 69 529 8 78 525 10 74 517 12 68 516 14 68 524 16 71 520 hi, anybody can tell me at here if Hydrogen bonds Refers to the middle column: 74,73,69,69,78,74,68,68,71 Thank you ! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/g-hbond-tp5008507.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] the -dist flag of g_hbond tool
Hi, See below On 24 May 2013, at 11:45, CHEN Pan evan.pan.c...@gmail.com wrote: Dear Gromacs users, I am confused about the g_hbond tools. 1) When I use -dist to get the distribution of hydrogen bonding distance, I found that the summation of the population is always 200 (the y-column below). I am not sure if it's was done with normalization or not, if yes, the summation should be one, if no, then the summation should equals to the total number of the hydrogen bonds, but here the hbnum.xvg shows me I have 440 hydrogen bonds. Why here is always 200, not matter what types of hydrogen bonds. How many donors do you have, and how many acceptors? 2) In my system, there are several different types of hydrogen bonds, such as intra-chain and inter-chain or intra-sheet and inter-sheet hydrogen bonds. Is there any smart way to separately calculate those hydrogen bonds? By using the index.ndx file, I could separate the intra-chain hydrogen bonds, then I can get the inter-chain ones using the total one minus the intra-chain one. It may be possible to do the same for the intra-sheet and the inter-sheet. However, this strategy seems complex. Did anybody have experience or ideas for this problem? Pan # This file was created Fri May 24 11:06:01 2013 # by the following command: # g_hbond -f /Users/panchen/gromacs.file/ch1-56/alpha/md-a-re.xtc -s /Users/panchen/gromacs.file/ch1-56/alpha/md-a.tpr -n ../ful.ndx -b 11000 -e 16000 -a 30 -r 0.35 -da -num -hbn -ang -dist -g # # g_hbond is part of G R O M A C S: # # Gromacs Runs One Microsecond At Cannonball Speeds # @title Hydrogen Bond Distribution @xaxis label Hydrogen - Acceptor Distance (nm) @yaxis label @TYPE xy 0.0025 0 0.0075 0 0.0125 0 0.0175 0 0.0225 0 0.0275 0 0.0325 0 0.0375 0 0.0425 0 0.0475 0 0.0525 0 0.0575 0 0.0625 0 0.0675 0 0.0725 0 0.0775 0 0.0825 0 0.0875 0 0.0925 0 0.0975 0 0.1025 0 0.1075 0 0.1125 0 0.1175 0 0.1225 0 0.1275 0 0.1325 0 0.1375 0 0.1425 0 0.1475 0 0.1525 0 0.1575 0 0.1625 0 0.1675 0 0.1725 0 0.1775 0 0.1825 0 0.1875 0 0.1925 0 0.1975 0 0.2025 0 0.2075 0 0.2125 0 0.2175 0 0.2225 0 0.2275 0 0.2325 0.00538632 0.2375 0.125501 0.24251.23562 0.24756.08295 0.252516.4279 0.257528.6597 0.262536.0576 0.2675 35.154 0.272528.1539 0.277519.8073 0.282512.4602 0.28757.23832 0.29254.06577 0.29752.15794 0.30251.14423 0.3075 0.588366 0.3125 0.310611 0.3175 0.163206 0.3225 0.0772039 0.3275 0.0411156 0.3325 0.0210066 0.3375 0.0113113 0.3425 0.00574541 0.3475 0.00502723 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] the -dist flag of g_hbond tool
Hm. That is peculiar. The source code has the answer of course. I can have a look next week to see why that is. Erik On 24 May 2013, at 14:11, CHEN Pan evan.pan.c...@gmail.com wrote: Hi, I have 512 donors and 1024 acceptors. I have just tested g_hbond with my standard crystal structure, which I should get 512 hydrogen bonds. And the output hbnum.xvg does show 512 hydrogen bonds, which is correct. But the hbdist.xvg file still shows that the summation of population is 200. 2013/5/24 Erik Marklund er...@xray.bmc.uu.se Hi, See below On 24 May 2013, at 11:45, CHEN Pan evan.pan.c...@gmail.com wrote: Dear Gromacs users, I am confused about the g_hbond tools. 1) When I use -dist to get the distribution of hydrogen bonding distance, I found that the summation of the population is always 200 (the y-column below). I am not sure if it's was done with normalization or not, if yes, the summation should be one, if no, then the summation should equals to the total number of the hydrogen bonds, but here the hbnum.xvg shows me I have 440 hydrogen bonds. Why here is always 200, not matter what types of hydrogen bonds. How many donors do you have, and how many acceptors? 2) In my system, there are several different types of hydrogen bonds, such as intra-chain and inter-chain or intra-sheet and inter-sheet hydrogen bonds. Is there any smart way to separately calculate those hydrogen bonds? By using the index.ndx file, I could separate the intra-chain hydrogen bonds, then I can get the inter-chain ones using the total one minus the intra-chain one. It may be possible to do the same for the intra-sheet and the inter-sheet. However, this strategy seems complex. Did anybody have experience or ideas for this problem? Pan # This file was created Fri May 24 11:06:01 2013 # by the following command: # g_hbond -f /Users/panchen/gromacs.file/ch1-56/alpha/md-a-re.xtc -s /Users/panchen/gromacs.file/ch1-56/alpha/md-a.tpr -n ../ful.ndx -b 11000 -e 16000 -a 30 -r 0.35 -da -num -hbn -ang -dist -g # # g_hbond is part of G R O M A C S: # # Gromacs Runs One Microsecond At Cannonball Speeds # @title Hydrogen Bond Distribution @xaxis label Hydrogen - Acceptor Distance (nm) @yaxis label @TYPE xy 0.0025 0 0.0075 0 0.0125 0 0.0175 0 0.0225 0 0.0275 0 0.0325 0 0.0375 0 0.0425 0 0.0475 0 0.0525 0 0.0575 0 0.0625 0 0.0675 0 0.0725 0 0.0775 0 0.0825 0 0.0875 0 0.0925 0 0.0975 0 0.1025 0 0.1075 0 0.1125 0 0.1175 0 0.1225 0 0.1275 0 0.1325 0 0.1375 0 0.1425 0 0.1475 0 0.1525 0 0.1575 0 0.1625 0 0.1675 0 0.1725 0 0.1775 0 0.1825 0 0.1875 0 0.1925 0 0.1975 0 0.2025 0 0.2075 0 0.2125 0 0.2175 0 0.2225 0 0.2275 0 0.2325 0.00538632 0.2375 0.125501 0.24251.23562 0.24756.08295 0.252516.4279 0.257528.6597 0.262536.0576 0.2675 35.154 0.272528.1539 0.277519.8073 0.282512.4602 0.28757.23832 0.29254.06577 0.29752.15794 0.30251.14423 0.3075 0.588366 0.3125 0.310611 0.3175 0.163206 0.3225 0.0772039 0.3275 0.0411156 0.3325 0.0210066 0.3375 0.0113113 0.3425 0.00574541 0.3475 0.00502723 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Pan Chen CERMAV-CNRS BP 53 38041 Grenoble Cedex 9 tel. +33 (0)4 76 03 76 12 fax. +33 (0)4 76 54 72 03 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ
Re: [gmx-users] the -dist flag of g_hbond tool
It used to be. I didn't realise it was still in the code. We experimented a bit with having a continuous bond criterion instead of a binary measure. It didn't do for us what we hoped it would so it was abandoned. I know that some people are using Espiniozas empirical formula for bond energy, however, so that code may be resurrected at some point. Erik On 24 May 2013, at 15:12, CHEN Pan evan.pan.c...@gmail.com wrote: Yes. I have looked at it already. I may need to spend time to understand it. By the way, in the source code, it seems some part are written for calculating hydrogen bonding energy, but I haven't see any flag command could give a output of hydrogen bonding energy file. Is it still under development? 2013/5/24 Erik Marklund er...@xray.bmc.uu.se Hm. That is peculiar. The source code has the answer of course. I can have a look next week to see why that is. Erik On 24 May 2013, at 14:11, CHEN Pan evan.pan.c...@gmail.com wrote: Hi, I have 512 donors and 1024 acceptors. I have just tested g_hbond with my standard crystal structure, which I should get 512 hydrogen bonds. And the output hbnum.xvg does show 512 hydrogen bonds, which is correct. But the hbdist.xvg file still shows that the summation of population is 200. 2013/5/24 Erik Marklund er...@xray.bmc.uu.se Hi, See below On 24 May 2013, at 11:45, CHEN Pan evan.pan.c...@gmail.com wrote: Dear Gromacs users, I am confused about the g_hbond tools. 1) When I use -dist to get the distribution of hydrogen bonding distance, I found that the summation of the population is always 200 (the y-column below). I am not sure if it's was done with normalization or not, if yes, the summation should be one, if no, then the summation should equals to the total number of the hydrogen bonds, but here the hbnum.xvg shows me I have 440 hydrogen bonds. Why here is always 200, not matter what types of hydrogen bonds. How many donors do you have, and how many acceptors? 2) In my system, there are several different types of hydrogen bonds, such as intra-chain and inter-chain or intra-sheet and inter-sheet hydrogen bonds. Is there any smart way to separately calculate those hydrogen bonds? By using the index.ndx file, I could separate the intra-chain hydrogen bonds, then I can get the inter-chain ones using the total one minus the intra-chain one. It may be possible to do the same for the intra-sheet and the inter-sheet. However, this strategy seems complex. Did anybody have experience or ideas for this problem? Pan # This file was created Fri May 24 11:06:01 2013 # by the following command: # g_hbond -f /Users/panchen/gromacs.file/ch1-56/alpha/md-a-re.xtc -s /Users/panchen/gromacs.file/ch1-56/alpha/md-a.tpr -n ../ful.ndx -b 11000 -e 16000 -a 30 -r 0.35 -da -num -hbn -ang -dist -g # # g_hbond is part of G R O M A C S: # # Gromacs Runs One Microsecond At Cannonball Speeds # @title Hydrogen Bond Distribution @xaxis label Hydrogen - Acceptor Distance (nm) @yaxis label @TYPE xy 0.0025 0 0.0075 0 0.0125 0 0.0175 0 0.0225 0 0.0275 0 0.0325 0 0.0375 0 0.0425 0 0.0475 0 0.0525 0 0.0575 0 0.0625 0 0.0675 0 0.0725 0 0.0775 0 0.0825 0 0.0875 0 0.0925 0 0.0975 0 0.1025 0 0.1075 0 0.1125 0 0.1175 0 0.1225 0 0.1275 0 0.1325 0 0.1375 0 0.1425 0 0.1475 0 0.1525 0 0.1575 0 0.1625 0 0.1675 0 0.1725 0 0.1775 0 0.1825 0 0.1875 0 0.1925 0 0.1975 0 0.2025 0 0.2075 0 0.2125 0 0.2175 0 0.2225 0 0.2275 0 0.2325 0.00538632 0.2375 0.125501 0.24251.23562 0.24756.08295 0.252516.4279 0.257528.6597 0.262536.0576 0.2675 35.154 0.272528.1539 0.277519.8073 0.282512.4602 0.28757.23832 0.29254.06577 0.29752.15794 0.30251.14423 0.3075 0.588366 0.3125 0.310611 0.3175 0.163206 0.3225 0.0772039 0.3275 0.0411156 0.3325 0.0210066 0.3375 0.0113113 0.3425 0.00574541 0.3475 0.00502723 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users
Re: [gmx-users] Solvent molecules within a certain distance of solute
g_hbond and g_hbond -contact Erik On 22 May 2013, at 05:37, Vishal Kumar Jaiswal vishal3...@gmail.com wrote: Hello gromacs users I performed a 1 ns simulation of N-isopropylamide in water. Now i wish to calculate the average no of water molecules(averaged over entire trajectory) within a certain distance of solute and no. of water molecules that form H-bonds with solute. Could you guide me as to what tools are appropriate for this Vishal Undergraduate student IITG -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] MSD and frequency of writing trajectories
Hi, For particles that diffuse more than half a box length between frames will appear as if they haven't moved much, assuming you have periodic boundary conditions. Erik On 22 May 2013, at 11:41, Anna Akinshina anna.akinsh...@manchester.ac.uk wrote: Dear Gromacs Users, I have a question interpreting obtained msd data. I need to calculate diffusion coefficient for a single argon atom in a box of water (500 molecules). During the calculations (50ns) I write both trr and xtc trajectories, but to save space I write trr for whole system very seldom (every 5 steps = 100 ps) but in xtc I have argon only (no water) and write more often (every 1000 steps = 2 ps). When I analysed the results using g_msd I was surprised that the msd curves obtained from trr and xtc trajectories differ a lot, what affect the resulting diffusion coefficients. If I save trr more often, like every 1 steps (20ps) the results from both files coincide. Does the msd results depend on how often you write trajectories? If yes, what frequency for writing the trajectories for future calculation of the diffusion coefficient would be reasonable and how long should be the calculations? Thanks you Anna --- Dr Anna Akinshina School of Chemical Engineering Analytical Science The University of Manchester, UK -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] RNA MD Simulation using GROMACS
Hi, To get useful help with this issue you need to provide a more informative description of what when wrong, i.e. what gromacs tool was invoked and what input was used. Erik On 20 May 2013, at 10:59, Pruthvi Bejugam pruthvi.n...@gmail.com wrote: Hi all, I want to perform a RNA (Just RNA no protein or DNA included) MD Simulation. Can anybody suggest me what are the general parameters should be used for the RNA MD Simulations. I know that AMBER and CHARMM force field work well for DNA and RNA. i have tried the RNA MD simulation using AMBER force field and it got failed and the error was FATAL error found no suitable atoms in the parameters. so, any one please help me out with this problem. Thanks In advance, -- Pruthvi Raj. B, JRF, Lab no. 9 (New Building), Computational and Systems Biology Lab, National Centre for Cell Science, UoP Campus, Ganeshkhind, Pune, Maharashtra, 411007 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Hydrogen Bond analysis using Gromacs
HI,
s0, s1,… is (xm)grace codes that refer to the different datasets in the file.
Gromacs prints the datasets as different columns. I suggest opening the file
with xmgrace -nxy yourxvgfile.xvg. As for the -life option, the results are
based on a too wimple kinetic model for most applications.
Erik
On 17 May 2013, at 08:21, Keerthana S.P Periasamy keerthanas...@yahoo.com
wrote:
Hai
In Hydrogen Bonding Analysis, I want to know about the the
interpretation of option -life and -ac (autocorrelation) I cannot
understand what the columns P(t) and t p(t) describe and how to interpret
this. Similarly after tagging -ac option in .xvg file I am getting@ s0
legend Ac\sfin sys\v{}\z{}(t)
@ s1 legend Ac(t)
@ s2 legend Cc\scontact,hb\v{}\z{}(t) @ s3 legend -dAc\sfs\v{}\z{}/dt
i also want to know what these s0 to s3 specify and how to interpret
this.Please help me to get cleared of my doubts so that I can continue
further. Thanks in Advance
with regardsKeerthanaPeriasamy
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Re: [gmx-users] Large number of solvent molecules
Hi,
Have a look at the following article. It describes a non-standard box type that
seems ideal for your application. I don't know what is the latest gromacs
version where it is implemented, however.
Author = {Wassenaar, TA and Mark, AE},
Title = {{The effect of box shape on the dynamic properties of proteins
simulated
under periodic boundary conditions}},
Journal = {{JOURNAL OF COMPUTATIONAL CHEMISTRY}},
Year = {{2006}},
Volume = {{27}},
Number = {{3}},
Pages = {{316-325}},
On 14 May 2013, at 07:44, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote:
Thank you Dr. Dallas. Yes I think the issue is that the starting
conformation is linear, as I want to study its folding properties. I tried
the same with helical starting conformation, and got around 11 water
molecules, which is still ok.
I am trying to find a way to simulate a 89 aa peptide in linear starting
conformation such that the simulation is practically feasible.
On Tue, May 14, 2013 at 10:45 AM, Dallas Warren
dallas.war...@monash.eduwrote:
From the box volume printed in the script output it appears you have a
box that is approximately a 28nm cube. And that size box requires a
significant number of water molecules to fill up, so that number you have
in there (~770,000) seems about correct.
If you want to have less water molecules, then you will need to make the
simulation cell smaller. Whether that is possible or not depends on what
you are looking to observe, how big the molecule you are solvating is etc.
Catch ya,
Dr. Dallas Warren
Drug Discovery Biology
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
+61 3 9903 9304
-
When the only tool you own is a hammer, every problem begins to resemble a
nail.
-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-
boun...@gromacs.org] On Behalf Of Nikunj Maheshwari
Sent: Tuesday, 14 May 2013 3:04 PM
To: Discussion list for GROMACS users
Subject: [gmx-users] Large number of solvent molecules
Dear all,
I am trying to see the folding of a 89 aa peptide. So I am setting up
the
system from linear conformation.
I gave the following commands to build the box and add the solvent
molecules.
editconf -f output.gro -c -d 1.0 -bt dodecahedron -o outbox.gro
genbox -cp outbox.gro -cs spc216.gro -p topol.top -o outh2o.gro
Reading solute configuration
Go Rough, Oppose Many Angry Chinese Serial killers
Containing 1440 atoms in 89 residues
Initialising van der waals distances...
WARNING: Masses and atomic (Van der Waals) radii will be guessed
based on residue and atom names, since they could not be
definitively assigned from the information in your input
files. These guessed numbers might deviate from the mass
and radius of the atom type. Please check the output
files if necessary.
Reading solvent configuration
216H2O,WATJP01,SPC216,SPC-
MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984
solvent configuration contains 648 atoms in 216 residues
Initialising van der waals distances...
Will generate new solvent configuration of 18x18x13 boxes
Generating configuration
Sorting configuration
Found 1 molecule type:
SOL ( 3 atoms): 909792 residues
Calculating Overlap...
box_margin = 0.315
Removed 324522 atoms that were outside the box
Neighborsearching with a cut-off of 0.48
Table routines are used for coulomb: FALSE
Table routines are used for vdw: FALSE
Cut-off's: NS: 0.48 Coulomb: 0.48 LJ: 0.48
System total charge: 0.000
Grid: 73 x 73 x 51 cells
Successfully made neighbourlist
nri = 3007232, nrj = 82473964
Checking Protein-Solvent overlap: tested 36005 pairs, removed 1653
atoms.
Checking Solvent-Solvent overlap: tested 7152003 pairs, removed 73182
atoms.
Added 776673 molecules
Generated solvent containing 2330019 atoms in 776673 residues
Writing generated configuration to outh2o.gro
Back Off! I just backed up outh2o.gro to ./#outh2o.gro.1#
Go Rough, Oppose Many Angry Chinese Serial killers
Output configuration contains 2331459 atoms in 776762 residues
Volume : 23276.3 (nm^3)
Density: 1001.32 (g/l)
Number of SOL molecules: 776673
Processing topology
Adding line for 776673 solvent molecules to topology file (topol.top)
Later on, I used -d 0.5. I still get around 71 water molecules in
the
system.
Then, I used g_mindist for both cases (d 1.0 and d 0.5). It is around 9
A
and 8.4 A respectively.
I need to know if I have done something wrong in setting up the system.
Is
there any way to get feasible number of solvent molecules?
Thanks
Nikunj
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Re: [gmx-users] Problem with DSSP
/home/dssp seems like a strange path. Are you sure you set DSSP correctly? Erik On 8 May 2013, at 15:19, Sainitin Donakonda saigr...@gmail.com wrote: Hello, I am trying to secondary structure analysis using DSSP in gromacs so i followed this procedure First I downloaded dssp wget ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.0.4-linux-amd64 -O ~/dssp this gave dssp executable file in my home directory I checked ./dssp ...it works Then i set environment variable as follows export DSSP=/myhomedir/dssp/dssp then i executed following command in gromacs do_dssp -f protein.xtc -s protein.tpr -sc scount.xvg -o ss.xpm -dt 10 But this gives following error *Program do_dssp, VERSION 4.5.4 Source code file: /home/toor/gromacs/gromacs-4.5.4/src/tools/do_dssp.c, line: 516 Fatal error: DSSP executable (/home/dssp) does not exist (use setenv DSSP)* * * *Can any body explain where it went wrong...* *I have gone through gromacs list but unfortunately couldnot manage to solve this simple issue* * * *Thanks,* *Nitin* -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] (no subject)
I really don't think thats possible at the moment. All interactions in Reax, if I recall correctly, are dependent on bond order, which is not an implemented concept in gromacs. Erik On 6 May 2013, at 12:51, Sathish Kumar sathishk...@gmail.com wrote: hai i would like to use Reax force field,can we use reax force field in gromacs and if any one please tell to me weather reax ff is useful for protein -- regards M.SathishKumar -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] constant protonation state MD
There's no general answer to that. Proton conductivity measurements, for instance, will be horribly wrong without dynamic protonation. Much (but not all) structural biology, however, will be largely unaffected. Erik On 3 May 2013, at 04:30, shahid nayeem msnay...@gmail.com wrote: Dear all Can someone enlighten me on the reliability of the results obtained from constant protonation state (assigned by different pKa value at different pH) MD simulation. Also want to know its reliability in case of implicit solvation model such as PB/GB calculation. Shahid -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] random seed in molecular dynamics
If I recall correctly it uses the seed provided in the mdp file. If no seed is provided it uses the process id for seeding. The manual explains the details. Erik On 3 May 2013, at 08:00, Preeti Choudhary preetichoudhary18111...@gmail.com wrote: hey this is regarding random seed used in md.this is when it selects the intial velocity and selects from maxwell-istribution.but is it selects only once or selects this random seed every time when grompp makes .tpr file.really confused about this random seed concept.can u clear my confusion?? -thanks -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] constant protonation state MD
I don't have one in mind. It's a delicate question and perhaps I shouldn't have phrased it the way I did. Nevertheless, the pKa of most side chains mean that their protonation will be dominated by one state for most pH values. pKa-shifts and complicated interplay between protonation and structure cause exceptions to this and you should be aware that such things may in some cases be important. Also consider the timescales of pH-depedent structural changes and the length of your simulations. You could check out the papers on lambda dynamics by C. Brooks III for an interesting take on sampling multiple protonation states. Best, Erik On 3 May 2013, at 14:05, shahid nayeem msnay...@gmail.com wrote: Thanks a lot Erik. Could I get some reference based on which you say that much of the structural biology will be largely unaffected. Shahid On Fri, May 3, 2013 at 1:05 PM, Erik Marklund er...@xray.bmc.uu.se wrote: There's no general answer to that. Proton conductivity measurements, for instance, will be horribly wrong without dynamic protonation. Much (but not all) structural biology, however, will be largely unaffected. Erik On 3 May 2013, at 04:30, shahid nayeem msnay...@gmail.com wrote: Dear all Can someone enlighten me on the reliability of the results obtained from constant protonation state (assigned by different pKa value at different pH) MD simulation. Also want to know its reliability in case of implicit solvation model such as PB/GB calculation. Shahid -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] constant protonation state MD
Yes that's what lambda dynamics does. I mentioned it since it addresses the interplay between protonation and structure. So to answer your original question: it depends. Erik On 3 May 2013, at 15:27, shahid nayeem msnay...@gmail.com wrote: If I know correctly in lambda dynamics the dynamics of protonation/deprotonation equilibria is accounted for while my question relates to the typical constant protonation MD where each titratable group remains in one protonation state throughout the simulation. Please educate me Shahid On Fri, May 3, 2013 at 6:22 PM, Erik Marklund er...@xray.bmc.uu.se wrote: I don't have one in mind. It's a delicate question and perhaps I shouldn't have phrased it the way I did. Nevertheless, the pKa of most side chains mean that their protonation will be dominated by one state for most pH values. pKa-shifts and complicated interplay between protonation and structure cause exceptions to this and you should be aware that such things may in some cases be important. Also consider the timescales of pH-depedent structural changes and the length of your simulations. You could check out the papers on lambda dynamics by C. Brooks III for an interesting take on sampling multiple protonation states. Best, Erik On 3 May 2013, at 14:05, shahid nayeem msnay...@gmail.com wrote: Thanks a lot Erik. Could I get some reference based on which you say that much of the structural biology will be largely unaffected. Shahid On Fri, May 3, 2013 at 1:05 PM, Erik Marklund er...@xray.bmc.uu.se wrote: There's no general answer to that. Proton conductivity measurements, for instance, will be horribly wrong without dynamic protonation. Much (but not all) structural biology, however, will be largely unaffected. Erik On 3 May 2013, at 04:30, shahid nayeem msnay...@gmail.com wrote: Dear all Can someone enlighten me on the reliability of the results obtained from constant protonation state (assigned by different pKa value at different pH) MD simulation. Also want to know its reliability in case of implicit solvation model such as PB/GB calculation. Shahid -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] vacum simulation
You seem to be using a 2 fs time step. It's difficult to achieve stable integration using 2 fs time steps in vacuum. Please provide more information about your simulation parameters. Erik On 2 May 2013, at 14:40, Souilem Safa safasouil...@gmail.com wrote: Dear Gromacs users , I did the simulation of a single molecule in vacum. I have choosed 10 ns which corresponds to 500 steps. I was checking the .log file frequently. I have noticed that the number of steps from 1938900 didn't increases. When I open a new tab with the top option, I see mdrun still existing. I have attached here the .log file and also some warnings that I saw when steps stop at 1938900 Step 1938969, time 3877.94 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 12871303501.643789, max 33207281664.00 (between atoms 3 and 6) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 46 47 98.80.1406 3889.8669 0.1000 45 46 79.4 10193.8799 10564.2393 0.1440 43 44 79.60.1033 631.2256 0.1000 42 45 80.1 10193.9062 11014.6123 0.1520 42 43 93.50.1851 4970.4243 0.1440 40 41 76.50.1009 184.9659 0.1000 39 42 90.40.1819 5231.5186 0.1520 39 40 100.00.1502 624.0559 0.1440 37 38 97.10.1001 592.4050 0.1000 36 37 81.40.1469 828.7896 0.1430 35 39 88.60.1742 8071.4395 0.1520 35 36 94.70.1861 8093.3452 0.1530 35 34 92.9 8046.3804 17904.5762 0.1440 33 45 78.0 26093.2402 332765.5000 0.1520 33 34 94.6 26065.5371 330302.5625 0.1440 29 30 74.4 190965.5938 1213272. 0.1360 27 28 91.2 85465.0547 294693.5000 0.1430 25 27 85.7 126649.9141 1143663.7500 0.1360 25 26 107.7 116051.3750 805165.8125 0.1230 24 29 102.8 1939418.3750 1702562.5000 0.1390 24 25 101.0 1963544.3750 1402288.3750 0.1390 22 23 97.9 345568.0625 1364901. 0.1530 31 21 109.7 1948370.1250 7003795.5000 0.1390 21 22 101.2 2108572.2500 6662917.5000 0.1390 20 24 89.4 8876732. 68351760. 0.1390 20 21 89.1 8780558. 67941296. 0.1390 20 19 88.5 39924512. 280068256. 0.1530 17 19 92.9 371385600. 509824768. 0.1530 17 18 96.4 394707616. 358144416. 0.1230 17 16 90.0 446916736. 883243840. 0.1360 15 16 98.9 1051905920. 370290400. 0.1430 14 15 100.8 520221760. 522257472. 0.1530 13 14 128.2 1139173888. 3275473920. 0.1390 13 11 155.0 2786396928. 3396753920. 0.1390 11 12 151.7 1220930176. 2911329792. 0.1090 9 11 161.5 369404096. 342864. 0.1390 9 10 135.8 2190610944. 1502276608. 0.1090 7 8 91.7 148944928. 1389486464. 0.1000 6 9 150.6 497182528. 4613532672. 0.1390 6 7 168.3 1652069120. 3562507776. 0.1360 4 5 165.5 55138408. 449667456. 0.1000 3 6 169.0 1702803200. 4615812096. 0.1390 3 4 124.7 198457328. 2500093184. 0.1360 13 1 158.1 1042088320. 3730094848. 0.1390 Wrote pdb files with previous and current coordinates Please I need your help what should I do in this case? Best regards, Safa -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] RMSD from the average structure
Average coordinates are problematic and not generally representative. Consider for instance the average coordinates of a methyl group connected to X. The rotation around the C-X bond causes the average positions of the hydrogens to line up. Consider using g_cluster to find representative structures from your trajectory. Erik On 26 Apr 2013, at 06:59, bipin singh bipinel...@gmail.com wrote: Thanks for your reply. Actually I am interested to see how much structural deviation is occurring in a protein during the simulation from its average position of atoms rather than the initial position (crystal structure or starting structure). The motivation of doing this analysis is the fact that in real solution phase, a system may not be static and if we consider the time average structure of a simulation to be the real representative of the structure in solution phase rather than static crystal structure. On Fri, Apr 26, 2013 at 2:06 AM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Bipin Singh, That indeed gives you the RMSD against the average. Do think about it a bit more: do you want the average of the whole structure, or should you account for a phase of relaxation? Cheers, Tsjerk On Wed, Apr 24, 2013 at 2:17 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/24/13 3:06 AM, bipin singh wrote: Hi all, Please let me know whether this is the right way to calculate RMSD from the average structure from a simulation: g_rmsf -f traj.xtc -s average.pdb -od rmsdev.xvg average.pdb: is the pdb file produced using -ox option of g_rmsf. You can calculate RMSD with respect to whatever structure you like, but the interpretation and justification for doing so are up to you. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- *--- Thanks and Regards, Bipin Singh* -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] any other criteria for h-bond?
Hi, Could you please clarify if the hbond existed in frames for which g_sdangle reported a ADH-angle above 30 deg? Also, bear in mind that the -merge flag is on by default, so another hydrogen may bridge the donor-acceptor gap. Erik On 24 Apr 2013, at 21:09, kim2811 kmani...@iastate.edu wrote: Hi, is there any other criteria in determining a hydrogen bond? i know that in order for a bond to exist, donor-acceptor distance should be less than or equal 3.5A and A-D-H angle less than or equal 30deg. I used g_sgangle to measure the angle A-D-H of two hydrogen bonds identified when I determined the hydrogen bonds using g_hbond. What I did is, I separated A-D and H-D as two groups (i made the atom indices in the order A-D and H-D in the index file) and measured the angle between these two vectors. However, the A-D-H angle as a function of time fall above the cut-off of 30deg and I wonder why. is there any other explanation for this? thank you. -- Kristine -- View this message in context: http://gromacs.5086.x6.nabble.com/any-other-criteria-for-h-bond-tp5007623.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] doubt in remd
The gromacs web page links to this server for REMD temperature generation: http://folding.bmc.uu.se/remd/ On 9 Apr 2013, at 08:34, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: Hi. Glad to know that your REMD was successful. We are trying to do the same, but are stuck in between. Can you tell us, how did you got the temperature spacing? Thanks On Tue, Apr 9, 2013 at 11:59 AM, Shine A shin...@iisertvm.ac.in wrote: Respected sir, I successfully completed REMD simulation. Now I am struggling with analysis part. Here how I select the global minimum from replica? Can you give some suggestions about the analysis part? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Maximum protein size for REMD?
I've tried one with 666 aa, but with no publishable results. On 9 Apr 2013, at 09:47, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: Dear all... Does anyone has any idea what is the maximum protein size for which a successful REMD run has taken place? We have went through lots of research papers, but could not find any protein/peptide above 100 aa related to REMD. We have a protein of 292 aa. Thanks. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Maximum protein size for REMD?
I used the REMD temperature generator. Needless to say, we got really tight spacing and the enhancement to the sampling was probably small. The whole setup was pretty experimental. The run was completed. Erik On 9 Apr 2013, at 10:01, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: How did you get the final temperature spacing for the run? Did you get the fitted values using polynomial fit? Was the run completed? On Tue, Apr 9, 2013 at 1:27 PM, Erik Marklund er...@xray.bmc.uu.se wrote: I've tried one with 666 aa, but with no publishable results. On 9 Apr 2013, at 09:47, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: Dear all... Does anyone has any idea what is the maximum protein size for which a successful REMD run has taken place? We have went through lots of research papers, but could not find any protein/peptide above 100 aa related to REMD. We have a protein of 292 aa. Thanks. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] autocorrelation function of hydrogen bond : g_hbond
There's a known oscillation in the ACF that occurs at ~100 fs or so. Is that what you see? Erik On 9 Apr 2013, at 18:02, Nilesh Dhumal ndhu...@andrew.cmu.edu wrote: On Tue, Apr 9, 2013 at 11:47 AM, Nilesh Dhumal ndhu...@andrew.cmu.eduwrote: Hello, I am calculating the hydrogen bond autocorrelation function using g_hbond for O-H---O hydrogen bond in system. I made two groups 1. O-H atoms numbers 2. two oxygen atoms are interacting with OH bond. I am using default hydrogen bond criteria (donor-acceptor distance 3.5 and angle 30) for calculating the autocorrelation function. I am not getting a smooth exponential plot. I get a small bump in the plot. Attached the autocorrelation plot. Attachments are not allowed on this list. Please provide a link to the image. Why there is not smooth exponential plot. There is no way to tell, and even with the image there is still no way to tell. How much sampling do you have? Have you looked at overall convergence, etc? I saved the trajectory at 3fs. It converged. Nilesh -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] COM restraint similar to distance restraints
It is, and I think there was in fact some experimental/private branch that dabbled with this. It hasn't gone into the official releases yet and there is no guarantee that it will. Erik On 4 Apr 2013, at 14:10, nahren manuel meetnah...@yahoo.com wrote: Sorry to bother you all once again. As there were no replies, I assume it is not possible to implement COM distance restraints in a way similar to distance restrains. nahren From: nahren manuel meetnah...@yahoo.com To: gromacs gromacs gmx-users@gromacs.org Sent: Monday, April 1, 2013 9:56 PM Subject: [gmx-users] COM restraint similar to distance restraints Dear Gromacs Users, I was wondering if there is a way to implement the COM distance restraints (which I presently apply using pull, and setting pull-rate =0.0) in way similar to distance restraints defining the lower up1 up2 (i.e harmonic restraint with a flat well). Any suggestion will be appreciated. Sincerely, nahren -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] -vsite in Umbrella sampling
I always do. There's nothing particular about umbrella sampling in this respect. On 4 Apr 2013, at 17:33, raghav singh raghavbioi...@gmail.com wrote: Hello Fellow Users, I have a question regarding US simulation. I am interested to know that can I treat hydrogens as virtual sites in US simulations?? I have very large protein complexes and to use higher time stepping during simulations...I am thinking to use -vsite option. what do you guys suggest?? Thank you Raghav -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_hbond
Yes. On 3 Apr 2013, at 04:07, Nilesh Dhumal ndhu...@andrew.cmu.edu wrote: Hello, I am calculating the hydrogen bond life time for my system. Do program consider the hydrogen bond criteria for calculation of autocorrelation function? Nilesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] REMD general protocol ...
On 2 Apr 2013, at 13:30, Justin Lemkul jalem...@vt.edu wrote: On 4/2/13 7:13 AM, rama david wrote: Dear friends, I am naive to the Replica exchange Molecular dynamics ( REMD). I have plan to use REMD for temp. 310-320 K to my system. I thoroughly search the Mailing-list Archive for the REMD problem. It was a really helpful to start. My system consist of peptide + water. I used the following work-flow, Would you please help me to find out my mistakes... 1. energy minimesation for peptide + solvent 2. Different Mdp file for temp. ( 4 temp therefore 4 mdp file ) 3. Make tpr file for each nvt run 4. Then separate equilibration for each temp ( 4 equilibration steps ) 5. Then made NPT.mdp file for each temp ( 4 temp ) 6. Then again equilibration for NPT at 4 temp.( 4 equilibration steps ) 7. Then run md production with -replex 1000 -multi 4 command .. To determine the temp I used web-server http://folding.bmc.uu.se/remd/ Please suggest me any improvements that are possible to implement in my work flow. Such a narrow range of temperatures defeats the purpose of using REMD. Normally, a much larger range is used over many more simulations. For near-ambient temperatures, NPT can be used, but if you include much higher temperatures, you should use NVT due to box instability upon exchanges. -Justin Sure, the enhanced sampling is basically gone, but you can deduce temperature dependences from such simulations and to some extent benefit from the mixing, can't you? Erik -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] scaling factor for rna/dna
Hi, I suggest contacting people in Johan Åqvist's lab. I'm sure they know exactly what pitfalls there may be with regards to the choice of LIE parameters and what has been done for different types of molecules. Erik On 26 Mar 2013, at 02:42, Vishwambhar Bhandare vishway...@gmail.com wrote: dear gromacs users, I am doing LIE calculation in gromacs for RNA molecules, What scaling factor (alpha and beta) should i use for calculation? Is that default values for protein ligand will work'? how we can get these alpha and beta scaling factors for nucleic acid? thanks in advance.. Thanks and Regards, -- Vishwambhar Centre for Bioinformatics Pondicherry University Pondicherry -- Note: Strictly confidential to Vishwayogi -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Hydrogen bonding differences
I could see how -merge (on by default) could lead to this. Have you tried -nomerge? Erik On Mar 22, 2013, at 4:46 PM, Kavyashree M wrote: Dear Users, As suggested earlier by Erik I used 4.6 to calculate the hydrogen bonds. Still the Total intra-protein hydrogen bonds is not equal (MM +MS +SS) hydrogen bond. Is there any other solution? Thank you Kavya On Fri, Jan 25, 2013 at 4:11 PM, Kavyashree M hmkv...@gmail.com wrote: Dear Sir, Sure I will try with 4.6. presently I am not able to download it. Thank you kavya On Fri, Jan 25, 2013 at 4:04 PM, Erik Marklund er...@xray.bmc.uu.sewrote: There were a handful of bugfixes to g_hbond over the last year. Could you try 4.6 or a smoking hot 4.5.5? I recognize this discrepancy form before. Erik On Jan 24, 2013, at 3:59 PM, Kavyashree M wrote: Dear Sir, This is 4.5.3. I have not tried nomerge. I did not use nomerge option in any of them, So if it has counted it (Hbond b/w same donor and acceptor but with different hydrogen) twice in one calculation then it will be counted twice in another, So wont the result with/without nomerge be the same? The difference is 4-5 Hbonds.. Thank you Kavya On Thu, Jan 24, 2013 at 7:30 PM, Erik Marklund er...@xray.bmc.uu.se wrote: Hi. What version was this? Have you tried with -nomerge? Erik On Jan 21, 2013, at 10:55 AM, Kavyashree M wrote: Dear users, While calculating hydrogen bonds for a simulation, it was found that the average number of intra protein hbonds was not equal to sum of MM, MS and SS hydrogen bonds. (MM - main chain - main chain, MS - main chain - side chain and side chain - side chain hydrogen bonds). There was a difference of 5 or so hbonds between intra-protein and MM+MS+SS hbonds. why is this so? I selected the options 7 7 for MM, 7 8 for MS and 8 8 for SS hydrogen bonds. One clarification. nhbdist option gives 0, 1, 2, 3 and total hydrogen bonds per hydrogen. Does this mean that a single hydrogen involving in forming hbond with 2 different acceptors/donors at different points of time in the trajectory. Thanks kavya -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchh**ttp://www.gromacs.org/Support/** Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists http://www.gromacs.org/**Support/Mailing_Lists http://**www.gromacs.org/Support/**Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchh**ttp://www.gromacs.org/Support/** Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists http://www.gromacs.org/**Support/Mailing_Lists http://**www.gromacs.org/Support/**Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http
Re: [gmx-users] Hydrogen bonding differences
I wouldn't say wrong, but I realized that some residue may make two hbonds to different parts of the protein, i.e. to the main chain and to a side chain at the same time. With -merge this counts as one if you analyze the entire protein. If you split your analysis such hbonds will show up in both e.g. SS and MS, hence TOT MM+SS+MS. It's just another way of counting hbonds. Erik On Mar 22, 2013, at 5:32 PM, Kavyashree M wrote: Sir, I tried -nomerge. It is fine now. But will it be wrong to calculate without nomerge option? Thank you Kavya On Fri, Mar 22, 2013 at 9:28 PM, Erik Marklund er...@xray.bmc.uu.se wrote: I could see how -merge (on by default) could lead to this. Have you tried -nomerge? Erik On Mar 22, 2013, at 4:46 PM, Kavyashree M wrote: Dear Users, As suggested earlier by Erik I used 4.6 to calculate the hydrogen bonds. Still the Total intra-protein hydrogen bonds is not equal (MM +MS +SS) hydrogen bond. Is there any other solution? Thank you Kavya On Fri, Jan 25, 2013 at 4:11 PM, Kavyashree M hmkv...@gmail.com wrote: Dear Sir, Sure I will try with 4.6. presently I am not able to download it. Thank you kavya On Fri, Jan 25, 2013 at 4:04 PM, Erik Marklund er...@xray.bmc.uu.se wrote: There were a handful of bugfixes to g_hbond over the last year. Could you try 4.6 or a smoking hot 4.5.5? I recognize this discrepancy form before. Erik On Jan 24, 2013, at 3:59 PM, Kavyashree M wrote: Dear Sir, This is 4.5.3. I have not tried nomerge. I did not use nomerge option in any of them, So if it has counted it (Hbond b/w same donor and acceptor but with different hydrogen) twice in one calculation then it will be counted twice in another, So wont the result with/without nomerge be the same? The difference is 4-5 Hbonds.. Thank you Kavya On Thu, Jan 24, 2013 at 7:30 PM, Erik Marklund er...@xray.bmc.uu.se wrote: Hi. What version was this? Have you tried with -nomerge? Erik On Jan 21, 2013, at 10:55 AM, Kavyashree M wrote: Dear users, While calculating hydrogen bonds for a simulation, it was found that the average number of intra protein hbonds was not equal to sum of MM, MS and SS hydrogen bonds. (MM - main chain - main chain, MS - main chain - side chain and side chain - side chain hydrogen bonds). There was a difference of 5 or so hbonds between intra-protein and MM+MS+SS hbonds. why is this so? I selected the options 7 7 for MM, 7 8 for MS and 8 8 for SS hydrogen bonds. One clarification. nhbdist option gives 0, 1, 2, 3 and total hydrogen bonds per hydrogen. Does this mean that a single hydrogen involving in forming hbond with 2 different acceptors/donors at different points of time in the trajectory. Thanks kavya -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/**mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/**listinfo/gmx-users h**ttp://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Search**h**ttp://www.gromacs.org/**Support/** http://www.gromacs.org/Support/** Mailing_Lists/Searchhttp://**www.gromacs.org/Support/** Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/** Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists http://**www.gromacs.org/**Support/**Mailing_Listshttp://www.gromacs.org/**Support/Mailing_Lists http://**www.gromacs.org/**Support/**Mailing_Listshttp://www.gromacs.org/Support/**Mailing_Lists http:/**/www.gromacs.org/Support/**Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/**mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/**listinfo/gmx-users h**ttp://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Search**h**ttp://www.gromacs.org/**Support/** http://www.gromacs.org/Support/** Mailing_Lists/Searchhttp://**www.gromacs.org/Support/** Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use thewww
Re: [gmx-users] Freezing some residues in equillibrium state?
On Mar 19, 2013, at 11:45 AM, Justin Lemkul wrote: On 3/19/13 5:44 AM, 라지브간디 wrote: Anyone tell me how do I freeze the particular residues in NPT-NVT equillibrium steps ? I want them in same conformation as pdb for further production run ? Thanks in advance Use freezegrps or strong position restraints. But note that if you release frozen groups after equilibration your system may need further time to equilibrate. Erik -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] pull code - constraint pulling - forces are zeros
Hi, I believe there is no force output for constraint pulling. Try umbrella. Erik On Mar 18, 2013, at 3:28 PM, raghav singh wrote: Hello Fellow Users, I am trying to pull a DNA molecule. I have fixed one end and trying to pull the other one using this .mdp file.. force output is all zeros. I have tried going through the user-list but have not found any solution yet. I am using gmx-version 4.5.5. Any idea why is it happening.?? below is the mdp file i am using. Thank you Raghav ## title = constraint pulling simulation define = -DPOSRES ; Run parameters integrator = md dt = 0.002 tinit = 0 nsteps = 2; 1ns nstcomm = 10 ; Output parameters nstxout = 100 ; every 10 ps nstvout = 100 nstfout = 20 nstxtcout = 20 ; every 1 ps nstenergy = 20 energygrps = DNA Water_and_ions ; Bond parameters constraint_algorithm= lincs lincs_iter = 1 lincs_order = 4 constraints = all-bonds continuation= no ; continuing from NPT ; Single-range cutoff scheme nstlist = 5 ns_type = grid rlist = 1.2 rcoulomb= 1.2 rvdw= 1.2 ; PME electrostatics parameters coulombtype = PME fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes ; Berendsen temperature coupling is on in two groups Tcoupl = V-rescale tc_grps = DNA Water_and_ions tau_t = 0.1 0.1 ref_t = 310 310 ; Pressure coupling is on Pcoupl = Parrinello-Rahman pcoupltype = isotropic tau_p = 2.0 compressibility = 4.5e-5 ref_p = 1.0 refcoord_scaling = com ; Generate velocities is off gen_vel = yes ; Periodic boundary conditions are on in all directions pbc = xyz ; Long-range dispersion correction DispCorr= EnerPres ; Pull code pull= constraint pull_geometry = distance ; simple distance increase pull_dim= N Y N pull_start = yes ; define initial COM distance 0 pull_ngroups= 1 pull_group0 = Fixed pull_group1 = Pull pull_rate1 = 0.001 ; 0.01 nm per ps = 10 nm per ns pull_k1 = 500 ### -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] MD in Vacuum
Hi, You also need to consider the ensemble you want to investigate. If you simulate under constant energy you need a shorter timestep than you would have in solution and probably double precision. In the articles I list below we used a timestep of 0.5 fs and 1 fs, respectively, and double precision. Monitor the total energy and you will see it drifting early on if you e.g. have a timestep that is too long. You could also try to apply the constraints more accurately than default. * Patriksson, A., Marklund, E., and Van der Spoel, D. (2007) Protein Structures under Electrospray Conditions. Biochemistry, 56(4):933pp * Marklund, E. G., Larsson, S. D., Patriksson, A., Van der Spoel, D., and Caleman, C. (2009) Structural stability of electrosprayed proteins: temperature and hydration effects. Physical Chemistry Chemical Physics, 11(36):8069pp Modesto Orozco and coworkers have also simulated biomolecules in the gas phase. I suggest to also have a look at their work. Best, On Mar 13, 2013, at 8:22 PM, Justin Lemkul wrote: On 3/13/13 12:53 PM, Lara Bunte wrote: Hello In all my tutorials for md they investigate a molecule in solution. I want to do md simulations in vacuum and I did not find a good tutorial. So I want to ask you what should I do for a md simulation in vaccum? Consult the literature. Tutorials will not cover every topic, and since most MD force fields were designed for condensed-phase simulations, it's awfully hard to explain to a new user why we're making wild changes to normal settings and hope that they understand :) I take a molecule, optimize the structure, generate a topology with gromacs and what after this? Do I also have to make a box? what is the procedure? Usually in vacuo simulations are done in the absence of periodicity and with infinite cutoffs. In general, an approach like the following is used: comm-mode = Angular nstlist = 0 rlist = 0 rvdw = 0 rcoulomb = 0 pbc = no ns-type = simple vdwtype = cutoff coulombtype = cutoff Check literature to be sure to establish a protocol with some basis in precedent. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] position restraints
Restraints allow, by definition, for slight deviations. Erik On Mar 14, 2013, at 12:51 PM, Shima Arasteh wrote: Dear gmx users, I want to use restraints on backbone of my protein to keep its secondary structure during minimization and equilibration steps. To do so, I generated backbone-restrain.itp and then included it to top file. Next, added define = -DPOSRES to minim.mdp file. After minimization, when I check the minimization output file, I saw that the backbone of input and output files are not exactly the same. Is there any step which I have not done to set the restraints correctly? Thanks in advance. Sincerely, Shima -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] template parallelization
Do you really mean compile time? If so, issue make -j X (where x is the number of jobs used for building). If you mean runtime then the easiest thing is to split your trajectory in parts and run the processes in parallel, then patch the results together. That's if the calculations can be done on a per-frame basis (i.e. embarrassingly parallelizable problems). Next in line is to wrap some performance critical loop(s) in OpenMP pragmas and link to the OpenMP libraries on your system. If you want others to benefit from the code you should adhere to the parallelization framework in gromacs, e.g. use gromacs' wrappers and preprocessor directives for OpenMP and MPI magic. The latter may be more trouble than it's worth if your analysis is only for a limited userbase. There is a framework underway in gromacs for parallel analysis tools, but as far as I know it's not finalized yet. Erik On Mar 14, 2013, at 2:22 PM, subhadipdas wrote: First, here my system : Cent Os 64 bits gcc : 4.4.6 fftw : 3.3.2 including SSE 2 I am writing a code to find out the number of five and six membered rings in structure I of hydrate . My code takes long time to compile for my 500ps trajectory . So my query is that can the template file be made to run in parallel fashion ? If so ,how -- View this message in context: http://gromacs.5086.n6.nabble.com/template-parallelization-tp5006320.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: template parallelization
Gromacs currently use OpenMP and/or MPI with it's own wrappers for parallel computation. There is a general framework being developed for parallelizing analysis tools, but I don't know the specifics and I beleive it's not ready for use yet. Is that helping you? Erik On Mar 14, 2013, at 3:20 PM, subhadipdas wrote: Sorry but i can't understand the part about parallelization framework in gromacs . Can you please elaborate on this -- View this message in context: http://gromacs.5086.n6.nabble.com/template-parallelization-tp5006320p5006323.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] reg binding free energy
On Mar 7, 2013, at 2:59 AM, Justin Lemkul wrote: On 3/6/13 8:57 PM, Vishwambhar Bhandare wrote: dear gromacs user, how i can do binding free energy calculation for RNA duplex in gromacs? any tutorial for the same?? Free energy calculations involving interactions between macromolecules are typically done with umbrella sampling. A tutorial is linked from gromacs.org, otherwise refer to the literature for suggested methodology. The challenge is likely to find a proper reaction coordinate and assure that you sample sufficiently along it. You may end up wasting a lot of computer time if you make a poor choice. Erik -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Time-Dependent Electric Field
From the manual it seems that oscillating electric fields are not yet implemented, which surprised me. I've seen colleagues use such in gromacs, but that may have been in-house modifications. Should be fairly simple to implement though. Erik On Mar 4, 2013, at 11:30 PM, raquick wrote: Gromacs users, I am trying to run a simulation with a time dependent electric field with frequency of around 16 GHz in the Z direction. What numbers should I put in the .mdp file following E-zt: for a field with this frequency? I have looked at the source code but cannot determine what units the frequency should be in. Currently, for electric Field I have the following: E-z = 1 .5 1 E-zt= 1 (some number) 0 I want to know what the some number should look like. Any help is appreciated. Regards, Ross Quick -- View this message in context: http://gromacs.5086.n6.nabble.com/Time-Dependent-Electric-Field-tp5006108.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_hbond and contact
To clarify: the -hbn output is not very indicative of how many contacts there were since some of them could be present in one frame but absent in 99. The -num option, however, provides the number of contacts over time, and its time average probably tells you much more in this case. What version of g_hbond are you using? I remember there were several bugfixes over the last 6 months or so. With the latest version(s) I believe that the -merge flag has no effect on contact analysis, which is correct. Erik On Mar 5, 2013, at 5:20 AM, Kavyashree M wrote: I am sorry There is no 7ws Its a typographic error. What I wanted to ask was - I am comparing two simulations S1 and S2 for contacts at a given cut off I used g_mdmat and g_hbond to calculate it. g_hbond outputs: of -num and -hbn was considered. 1. -hbn output was analysed to calculate how many contacts each atom has from both S1 and S2. 2. -num output graph was compared from both S1 and S2. g_mdmat output: of -no was considered. 3. -no output was analysed from both S1 and S2 using the third column or the second Y value which gives total contacts of each atom. It was observed that 1 and 3 matched exactly giving the same number of contacts each atom has (in the whole simulations). indicating that the number of contacts each atom has was more in S2 than S1. But the graph from 2 indicated that the number of contacts (along the trajectory) in S1 was higher than S2. My doubt is: The number of contact per atom follows S2 S1 while number of contacts per time follows S1 S2. I am unclear as to what I have to conclude from this observations. - I used the same cutoff throughout. - There has not been any swapping of the trajectory while analysing. Thank you Kavya On Tue, Mar 5, 2013 at 1:09 AM, Justin Lemkul jalem...@vt.edu wrote: On 3/4/13 1:10 PM, Kavyashree M wrote: On Mon, Mar 4, 2013 at 11:10 PM, Justin Lemkul jalem...@vt.edu wrote: When measuring contacts, you don't measure one group, you measure the number of contacts that occur between groups A and B, which considers all atoms in those two groups. I gave a group of hydrophobic atoms in both cases The command I gave - g_hbond_46 -fx.xtc-s x.tpr-contact -n x.ndx - r 0.4 -hbm o.xpm -hbn o.ndx -num o.xvg my index file contained a group of hydrophobic atoms. which I supplied in the x.ndx. You don't define contacts in an index group, you define atoms that may or may not make contacts with others. The one I mentioned here is the output index file from the g_hbond (4.6 version) - o.ndx. [ contacts_C_CA_CB_CD_CD1_CD2_CE_CE1_CE2_CE3_CG_CG1_CG2_CZ_*** *CZ2_CZ3_CH2 ] 5 7ws 5 10 5 14 5 18 5 22 5 24 5 27 5 30 5 35 5292 5296 530 There's something very wrong with this index file. How did you generate it? The presence of a repeated atom number (5) and a nonsensical one (7ws) leads me to believe that you've done something incorrect. Did this come from g_hbond? It looks like the output of -hbn, which is only useful for decoding hbmap.xpm, nothing else. I did not generate this. The tool (g_hbond) generated this index file. It is the -hbn output. OK, then I still don't know what 7ws is, but the only purpose for this file is to provide a key to the existence matrix in hbmap.xpm. Your previous description indicated that you were using it for some other analysis, which would not be appropriate. The other thing worth mentioning here is something that was posted to the list just a few hours ago, that the output of g_hbond -contact may not agree with other methods of calculating contacts, especially in the case of -merge vs. -nomerge. -Justin From this second section Total contacts was extracted for each atom and compared with that from a second simulation. These contacts was matching with the contacts of the 3rd column from g_mdmat output - @ legend string 0 Total/mean @ legend string 1 Total @ legend string 2 Mean @ legend string 3 # atoms @ legend string 4 Mean/# atoms #resratio tot mean natm mean/atm 1 1.001 1110.991110.991 2 1.244 10 8.0411 8.041 3 1.166 1311.147111.147 4 1.036 1110.615110.615 While the time dependent contacts in the xvg file shows that the first simulation has more contacts than the second one.. That shouldn't be unexpected. Two independent simulations have no guarantee of doing the same thing, that's why sampling is so important. Thank you kavya -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540)
Re: [gmx-users] g_hbond and contact
On Mar 5, 2013, at 10:34 AM, Kavyashree M wrote: Sir, I used gromacs 4.6. I got the point - index file will tell how many contacts an atom has made during the trajectory. Whether it has made a contact with an atom only in once or all the time, in the whole trajectory, it will be mentioned. Am I right? Yes. So from the problem I had, can I say that no. of contact/atom had increased in S2 while the no. of contact/time decreased? That depends. If 'contact' means unique interactions and 'atom' means e.g. all atoms in in your system, then yes. Its a bit confusing though! Thank you kavya On Tue, Mar 5, 2013 at 2:26 PM, Erik Marklund er...@xray.bmc.uu.se wrote: To clarify: the -hbn output is not very indicative of how many contacts there were since some of them could be present in one frame but absent in 99. The -num option, however, provides the number of contacts over time, and its time average probably tells you much more in this case. What version of g_hbond are you using? I remember there were several bugfixes over the last 6 months or so. With the latest version(s) I believe that the -merge flag has no effect on contact analysis, which is correct. Erik -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Difference in Number of contacts through g_hbond and g_mindist
As Justin implied, -merge could potentially make a factor of 2. Try g_hbond -nomerge. Erik On Mar 4, 2013, at 4:02 PM, bipin singh wrote: Thanks for the reply. The difference is almost double, through g_hbond the average number of contacts are 1821 and through g_mindist it is 3643. The calculation group does not contains hydrogen atoms. On Mon, Mar 4, 2013 at 8:14 PM, Justin Lemkul jalem...@vt.edu wrote: On 3/4/13 9:08 AM, bipin singh wrote: Hi All, I have a doubt regarding the calculation of number of contacts between two groups. Because, I am getting different number of contacts calculated through g_hbond -contact option and g_mindist -on option. I have used same cutoff for distance (0.6nm) in both the cases. How different are the results? The g_hbond code is very complex, but you'd probably have to go into the inner workings of both programs to understand why. I also do not know whether other settings in g_hbond will matter, like -merge, or whether or not g_hbond will only calculate contacts among H-bond participating groups. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- *--- Thanks and Regards, Bipin Singh* -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] do_dssp
Hi, I'll try out the 2.1.0 with do_dssp and see if there's something problematic with this new version. Good thing you brought it up. Erik On Mar 1, 2013, at 6:24 PM, Miguel Ángel Mompeán García wrote: Hi Erik, Since I read in the mailing list that nobody had asked about 2.1.0, just decided to try an older version before going into the trouble itself... Kind of coward, I know, but the troubles with that version are already reported so that I thought things would be easier :) Thank-you a lot for your comments 2013/3/1 Erik Marklund er...@xray.bmc.uu.se Interesting. Perhaps there are new issues with 2.1.0. Did you try to execute the command yourself? Erik On Mar 1, 2013, at 5:16 PM, Miguel Ángel Mompeán García wrote: The issue I mentioned was with dssp-2.1.0. I changed to 2.0.1 and it works fine. However, when converting the xpm to eps I get I plot very small, where one barely can see the colour code and the legend is sooo big. Does anyone know how to change that? 2013/3/1 Erik Marklund er...@xray.bmc.uu.se What happens if you execute the command (/usr/local/bin/dssp/ -i ddQ3PqtX -o ddR1HavD) in your terminal? Erik On Mar 1, 2013, at 1:06 PM, Miguel Ángel Mompeán García wrote: I am using gromacs 4.6 and dssp-2.1.0 and I am getting that error you got: dssp cmd='/usr/local/bin/dssp/ -i ddQ3PqtX -o ddR1HavD /dev/ null 2 /dev/null' Reading frame 0 time0.000 Back Off! I just backed up ddQ3PqtX to ./#ddQ3PqtX.1# --- Program do_dssp, VERSION 4.6 Source code file: /usr/local/bin/gromacs-4.6/ src/tools/gmx_do_dssp.c, line: 667 Fatal error: Failed to execute command: Try specifying your dssp version with the -ver option. How can I fix that? Thanks 2013/1/15 James Starlight jmsstarli...@gmail.com Justin, thanks both options works perfect. James 2013/1/15 Justin Lemkul jalem...@vt.edu: On 1/15/13 7:13 AM, James Starlight wrote: Justin, I want to obtain timescale on X as well as number of residues on Y on the xmp graph . By default that graph has not legend so it's hard to analyse it . The legends are printed in the .xvg header. I've never had a problem plotting its contents (though they are usually somewhat unclear when plotted together) with xmgrace -nxy scount.xvg By the way have you forced with some problems with dppc ? Simetimes I've obtain error like There are 286 residues in your selected group dssp cmd='/usr/local/bin/dssp -i dd42GVbd -o ddpu8ln2 /dev/ null 2 /dev/null' Reading frame 0 time0.000 Back Off! I just backed up dd42GVbd to ./#dd42GVbd.1 Fatal error: Failed to execute command: Try specifying your dssp version with the -ver option. and I dont know how to fix it. I'm using gromacs-4.6-beta 3 with dssp 2.0.3 Since dssp changed its command line options, Gromacs had to adapt as well. The error tells you to use the -ver option; you should do so. Version 2 should be the default, so check to make sure you're actually using that version and not the old dssp. -Justin -- ==== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justinhttp://vt.edu/Pages/Personal/justin h**ttp://www.bevanlab.biochem.vt.**edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Searchhttp://www.gromacs.org/**Support/Mailing_Lists/Search h**ttp://www.gromacs.org/Support/**Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists http://www.gromacs.org/**Support/Mailing_Lists http://**www.gromacs.org/Support/**Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Searchhttp://www.gromacs.org/**Support/Mailing_Lists/Search h**ttp://www.gromacs.org/Support/**Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Search before
Re: [gmx-users] removing number of sol
If you have a pdb file instead of a gro file then e.g. pymol might be useful. Erik On Mar 2, 2013, at 2:01 PM, gromacs query wrote: Dear Erik, I am new to Gromacs and used AMBER before, and I am exploring various options in GROMACS too. Surely I will look in to g_select. Also as I was using sed, one should include an extra space (using vi) in gro file just before residue number and then can use sed to remove like this: sed - e '/ 35SOL/d' -e '/ 36SOL/d' -e '/ 38SOL/d' -e '/ 39SOL/d' old.gro new2.gro But please note I included an extra space / 35SOL/d (instead of / 35SOL/d) by this sed will remove 35SOL not 135SOL. regards, On Fri, Mar 1, 2013 at 5:27 PM, Erik Marklund er...@xray.bmc.uu.se wrote: Hi, Then the problem lies in automating what molecules are to be removed, right? Try g_select or look into trjorder. Erik On Mar 1, 2013, at 2:45 PM, gromacs query wrote: Aha! thanks Erik (and Justin), I really feel sorry 35 and 135 will be removed by sed. I must have given a thought about that. So this was reason sed was over doing the things. Also as you asked: They are random residue number water molecules so not continuous and they were selected on the criteria based on X Y Z coordinates (some space fixed and outlier waters are to be removed) regards, On Fri, Mar 1, 2013 at 3:09 PM, Erik Marklund er...@xray.bmc.uu.se wrote: On Mar 1, 2013, at 2:08 PM, Erik Marklund wrote: On Mar 1, 2013, at 1:58 PM, gromacs query wrote: Dear Erik, so you can filter out the unwanted residues there instead of using an index file. There are thousands of water to be removed so simple commands like sed exhausts when I run it in loops. e.g. Just to say : sed -e '/35SOL/d' -e '/36SOL/d' -e '/38SOL/d' -e '/39SOL/d' -e '/40SOL/d' -e '/41SOL/d' -e '/42SOL/d' -e '/43SOL/d' -e '/44SOL/d' -e '/ 45SOL/d' old.gro new2.gro this will remove such 10 residues but if you run this again and again (in text exe format) say 1000 times it exhausts some how and remove waters which are not even mentioned in sed command! I have checked it many times. So I thought if index file could help me. But please reply for point 3: First of all, that's not a safe way of removing waters. Note that both SOL 35, SOL 135, ... will be removed by that command. Secondly, I'm sure you can think of a better way of scripting it, using e.g. sed or awk. By which criteria do you select the waters to be removed? If its a contiguous chunk then it's dead simple. 3) Also once I get index file can editconf help to write a new gro without the residues mentioned in index file?. I used this editconf -f my.gro -n index.ndx -o del.gro . thanks, This gave me del.gro having residues mentioned in index file. But I want del.gro file without the residues mentioned in index file. On Fri, Mar 1, 2013 at 2:48 PM, Erik Marklund er...@xray.bmc.uu.se wrote: The ndx format is really simple. You can easily script your way to a new index group as long as the selection of atoms can be automated. Furthermore, the gro format is also simple, so you can filter out the unwanted residues there instead of using an index file. Erik On Mar 1, 2013, at 1:42 PM, gromacs query wrote: Dear All, I know the residue numbers of SOL molecules (which are more than thousands) which I want to remove them from a gro file. I searched that make_ndx can be used make a index file to define residues. But It is a prompt based tool and its difficult to type manually thousands of residue numbers. 1) Is there some way to feed the residue numbers to make_ndx? Or I need to make index file format my self by some scritpting Or is there is rather easier way of doing in gromacs. 2) Also is there any direct command which helps to remove a residue number directly from a gro file without using index file input; means residue defined in command itself? 3) Also once I get index file can editconf help to write a new gro without the residues mentioned in index file?. I used this editconf - f my.gro -n index.ndx -o del.gro . This gave me del.gro having residues mentioned in index file. But I want del.gro file without the residues mentioned in index file. regards, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/**mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/**listinfo/gmx-users h**ttp://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Search**h**ttp://www.gromacs.org/**Support/** http://www.gromacs.org/Support/** Mailing_Lists/Searchhttp://**www.gromacs.org/Support
Re: [gmx-users] do_dssp
With -ver, just like it says. do_dssp -h explains how. What dssp version do you have? Erik On Mar 1, 2013, at 1:06 PM, Miguel Ángel Mompeán García wrote: I am using gromacs 4.6 and dssp-2.1.0 and I am getting that error you got: dssp cmd='/usr/local/bin/dssp/ -i ddQ3PqtX -o ddR1HavD /dev/null 2 /dev/null' Reading frame 0 time0.000 Back Off! I just backed up ddQ3PqtX to ./#ddQ3PqtX.1# --- Program do_dssp, VERSION 4.6 Source code file: /usr/local/bin/gromacs-4.6/src/tools/ gmx_do_dssp.c, line: 667 Fatal error: Failed to execute command: Try specifying your dssp version with the -ver option. How can I fix that? Thanks 2013/1/15 James Starlight jmsstarli...@gmail.com Justin, thanks both options works perfect. James 2013/1/15 Justin Lemkul jalem...@vt.edu: On 1/15/13 7:13 AM, James Starlight wrote: Justin, I want to obtain timescale on X as well as number of residues on Y on the xmp graph . By default that graph has not legend so it's hard to analyse it . The legends are printed in the .xvg header. I've never had a problem plotting its contents (though they are usually somewhat unclear when plotted together) with xmgrace -nxy scount.xvg By the way have you forced with some problems with dppc ? Simetimes I've obtain error like There are 286 residues in your selected group dssp cmd='/usr/local/bin/dssp -i dd42GVbd -o ddpu8ln2 /dev/null 2 /dev/null' Reading frame 0 time0.000 Back Off! I just backed up dd42GVbd to ./#dd42GVbd.1 Fatal error: Failed to execute command: Try specifying your dssp version with the -ver option. and I dont know how to fix it. I'm using gromacs-4.6-beta 3 with dssp 2.0.3 Since dssp changed its command line options, Gromacs had to adapt as well. The error tells you to use the -ver option; you should do so. Version 2 should be the default, so check to make sure you're actually using that version and not the old dssp. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] removing number of sol
The ndx format is really simple. You can easily script your way to a new index group as long as the selection of atoms can be automated. Furthermore, the gro format is also simple, so you can filter out the unwanted residues there instead of using an index file. Erik On Mar 1, 2013, at 1:42 PM, gromacs query wrote: Dear All, I know the residue numbers of SOL molecules (which are more than thousands) which I want to remove them from a gro file. I searched that make_ndx can be used make a index file to define residues. But It is a prompt based tool and its difficult to type manually thousands of residue numbers. 1) Is there some way to feed the residue numbers to make_ndx? Or I need to make index file format my self by some scritpting Or is there is rather easier way of doing in gromacs. 2) Also is there any direct command which helps to remove a residue number directly from a gro file without using index file input; means residue defined in command itself? 3) Also once I get index file can editconf help to write a new gro without the residues mentioned in index file?. I used this editconf -f my.gro -n index.ndx -o del.gro . This gave me del.gro having residues mentioned in index file. But I want del.gro file without the residues mentioned in index file. regards, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] do_dssp
What happens if you execute the command (/usr/local/bin/dssp/ -i ddQ3PqtX -o ddR1HavD) in your terminal? Erik On Mar 1, 2013, at 1:06 PM, Miguel Ángel Mompeán García wrote: I am using gromacs 4.6 and dssp-2.1.0 and I am getting that error you got: dssp cmd='/usr/local/bin/dssp/ -i ddQ3PqtX -o ddR1HavD /dev/null 2 /dev/null' Reading frame 0 time0.000 Back Off! I just backed up ddQ3PqtX to ./#ddQ3PqtX.1# --- Program do_dssp, VERSION 4.6 Source code file: /usr/local/bin/gromacs-4.6/src/tools/ gmx_do_dssp.c, line: 667 Fatal error: Failed to execute command: Try specifying your dssp version with the -ver option. How can I fix that? Thanks 2013/1/15 James Starlight jmsstarli...@gmail.com Justin, thanks both options works perfect. James 2013/1/15 Justin Lemkul jalem...@vt.edu: On 1/15/13 7:13 AM, James Starlight wrote: Justin, I want to obtain timescale on X as well as number of residues on Y on the xmp graph . By default that graph has not legend so it's hard to analyse it . The legends are printed in the .xvg header. I've never had a problem plotting its contents (though they are usually somewhat unclear when plotted together) with xmgrace -nxy scount.xvg By the way have you forced with some problems with dppc ? Simetimes I've obtain error like There are 286 residues in your selected group dssp cmd='/usr/local/bin/dssp -i dd42GVbd -o ddpu8ln2 /dev/null 2 /dev/null' Reading frame 0 time0.000 Back Off! I just backed up dd42GVbd to ./#dd42GVbd.1 Fatal error: Failed to execute command: Try specifying your dssp version with the -ver option. and I dont know how to fix it. I'm using gromacs-4.6-beta 3 with dssp 2.0.3 Since dssp changed its command line options, Gromacs had to adapt as well. The error tells you to use the -ver option; you should do so. Version 2 should be the default, so check to make sure you're actually using that version and not the old dssp. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] removing number of sol
On Mar 1, 2013, at 1:58 PM, gromacs query wrote: Dear Erik, so you can filter out the unwanted residues there instead of using an index file. There are thousands of water to be removed so simple commands like sed exhausts when I run it in loops. e.g. Just to say : sed -e '/35SOL/d' -e '/36SOL/d' -e '/38SOL/d' -e '/39SOL/d' -e '/ 40SOL/d' -e '/41SOL/d' -e '/42SOL/d' -e '/43SOL/d' -e '/44SOL/d' -e '/45SOL/d' old.gro new2.gro this will remove such 10 residues but if you run this again and again (in text exe format) say 1000 times it exhausts some how and remove waters which are not even mentioned in sed command! I have checked it many times. So I thought if index file could help me. But please reply for point 3: First of all, that's not a safe way of removing waters. Note that both SOL 35, SOL 135, ... will be removed by that command. Secondly, I'm sure you can think of a better way of scripting it, using e.g. sed or awk. By which criteria do you select the waters to be removed? 3) Also once I get index file can editconf help to write a new gro without the residues mentioned in index file?. I used this editconf -f my.gro -n index.ndx -o del.gro . thanks, This gave me del.gro having residues mentioned in index file. But I want del.gro file without the residues mentioned in index file. On Fri, Mar 1, 2013 at 2:48 PM, Erik Marklund er...@xray.bmc.uu.se wrote: The ndx format is really simple. You can easily script your way to a new index group as long as the selection of atoms can be automated. Furthermore, the gro format is also simple, so you can filter out the unwanted residues there instead of using an index file. Erik On Mar 1, 2013, at 1:42 PM, gromacs query wrote: Dear All, I know the residue numbers of SOL molecules (which are more than thousands) which I want to remove them from a gro file. I searched that make_ndx can be used make a index file to define residues. But It is a prompt based tool and its difficult to type manually thousands of residue numbers. 1) Is there some way to feed the residue numbers to make_ndx? Or I need to make index file format my self by some scritpting Or is there is rather easier way of doing in gromacs. 2) Also is there any direct command which helps to remove a residue number directly from a gro file without using index file input; means residue defined in command itself? 3) Also once I get index file can editconf help to write a new gro without the residues mentioned in index file?. I used this editconf -f my.gro -n index.ndx -o del.gro . This gave me del.gro having residues mentioned in index file. But I want del.gro file without the residues mentioned in index file. regards, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] removing number of sol
On Mar 1, 2013, at 2:08 PM, Erik Marklund wrote: On Mar 1, 2013, at 1:58 PM, gromacs query wrote: Dear Erik, so you can filter out the unwanted residues there instead of using an index file. There are thousands of water to be removed so simple commands like sed exhausts when I run it in loops. e.g. Just to say : sed -e '/35SOL/d' -e '/36SOL/d' -e '/38SOL/d' -e '/39SOL/d' -e '/ 40SOL/d' -e '/41SOL/d' -e '/42SOL/d' -e '/43SOL/d' -e '/44SOL/d' -e '/45SOL/d' old.gro new2.gro this will remove such 10 residues but if you run this again and again (in text exe format) say 1000 times it exhausts some how and remove waters which are not even mentioned in sed command! I have checked it many times. So I thought if index file could help me. But please reply for point 3: First of all, that's not a safe way of removing waters. Note that both SOL 35, SOL 135, ... will be removed by that command. Secondly, I'm sure you can think of a better way of scripting it, using e.g. sed or awk. By which criteria do you select the waters to be removed? If its a contiguous chunk then it's dead simple. 3) Also once I get index file can editconf help to write a new gro without the residues mentioned in index file?. I used this editconf -f my.gro -n index.ndx -o del.gro . thanks, This gave me del.gro having residues mentioned in index file. But I want del.gro file without the residues mentioned in index file. On Fri, Mar 1, 2013 at 2:48 PM, Erik Marklund er...@xray.bmc.uu.se wrote: The ndx format is really simple. You can easily script your way to a new index group as long as the selection of atoms can be automated. Furthermore, the gro format is also simple, so you can filter out the unwanted residues there instead of using an index file. Erik On Mar 1, 2013, at 1:42 PM, gromacs query wrote: Dear All, I know the residue numbers of SOL molecules (which are more than thousands) which I want to remove them from a gro file. I searched that make_ndx can be used make a index file to define residues. But It is a prompt based tool and its difficult to type manually thousands of residue numbers. 1) Is there some way to feed the residue numbers to make_ndx? Or I need to make index file format my self by some scritpting Or is there is rather easier way of doing in gromacs. 2) Also is there any direct command which helps to remove a residue number directly from a gro file without using index file input; means residue defined in command itself? 3) Also once I get index file can editconf help to write a new gro without the residues mentioned in index file?. I used this editconf -f my.gro -n index.ndx -o del.gro . This gave me del.gro having residues mentioned in index file. But I want del.gro file without the residues mentioned in index file. regards, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests
Re: [gmx-users] removing number of sol
Hi, Then the problem lies in automating what molecules are to be removed, right? Try g_select or look into trjorder. Erik On Mar 1, 2013, at 2:45 PM, gromacs query wrote: Aha! thanks Erik (and Justin), I really feel sorry 35 and 135 will be removed by sed. I must have given a thought about that. So this was reason sed was over doing the things. Also as you asked: They are random residue number water molecules so not continuous and they were selected on the criteria based on X Y Z coordinates (some space fixed and outlier waters are to be removed) regards, On Fri, Mar 1, 2013 at 3:09 PM, Erik Marklund er...@xray.bmc.uu.se wrote: On Mar 1, 2013, at 2:08 PM, Erik Marklund wrote: On Mar 1, 2013, at 1:58 PM, gromacs query wrote: Dear Erik, so you can filter out the unwanted residues there instead of using an index file. There are thousands of water to be removed so simple commands like sed exhausts when I run it in loops. e.g. Just to say : sed -e '/35SOL/d' -e '/36SOL/d' -e '/38SOL/d' -e '/39SOL/d' -e '/ 40SOL/d' -e '/41SOL/d' -e '/42SOL/d' -e '/43SOL/d' -e '/44SOL/d' -e '/ 45SOL/d' old.gro new2.gro this will remove such 10 residues but if you run this again and again (in text exe format) say 1000 times it exhausts some how and remove waters which are not even mentioned in sed command! I have checked it many times. So I thought if index file could help me. But please reply for point 3: First of all, that's not a safe way of removing waters. Note that both SOL 35, SOL 135, ... will be removed by that command. Secondly, I'm sure you can think of a better way of scripting it, using e.g. sed or awk. By which criteria do you select the waters to be removed? If its a contiguous chunk then it's dead simple. 3) Also once I get index file can editconf help to write a new gro without the residues mentioned in index file?. I used this editconf -f my.gro -n index.ndx -o del.gro . thanks, This gave me del.gro having residues mentioned in index file. But I want del.gro file without the residues mentioned in index file. On Fri, Mar 1, 2013 at 2:48 PM, Erik Marklund er...@xray.bmc.uu.se wrote: The ndx format is really simple. You can easily script your way to a new index group as long as the selection of atoms can be automated. Furthermore, the gro format is also simple, so you can filter out the unwanted residues there instead of using an index file. Erik On Mar 1, 2013, at 1:42 PM, gromacs query wrote: Dear All, I know the residue numbers of SOL molecules (which are more than thousands) which I want to remove them from a gro file. I searched that make_ndx can be used make a index file to define residues. But It is a prompt based tool and its difficult to type manually thousands of residue numbers. 1) Is there some way to feed the residue numbers to make_ndx? Or I need to make index file format my self by some scritpting Or is there is rather easier way of doing in gromacs. 2) Also is there any direct command which helps to remove a residue number directly from a gro file without using index file input; means residue defined in command itself? 3) Also once I get index file can editconf help to write a new gro without the residues mentioned in index file?. I used this editconf -f my.gro -n index.ndx -o del.gro . This gave me del.gro having residues mentioned in index file. But I want del.gro file without the residues mentioned in index file. regards, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchh**ttp://www.gromacs.org/Support/** Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists http://www.gromacs.org/**Support/Mailing_Lists http://**www.gromacs.org/Support/**Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchh**ttp://www.gromacs.org/Support/** Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http
Re: [gmx-users] do_dssp
Interesting. Perhaps there are new issues with 2.1.0. Did you try to execute the command yourself? Erik On Mar 1, 2013, at 5:16 PM, Miguel Ángel Mompeán García wrote: The issue I mentioned was with dssp-2.1.0. I changed to 2.0.1 and it works fine. However, when converting the xpm to eps I get I plot very small, where one barely can see the colour code and the legend is sooo big. Does anyone know how to change that? 2013/3/1 Erik Marklund er...@xray.bmc.uu.se What happens if you execute the command (/usr/local/bin/dssp/ -i ddQ3PqtX -o ddR1HavD) in your terminal? Erik On Mar 1, 2013, at 1:06 PM, Miguel Ángel Mompeán García wrote: I am using gromacs 4.6 and dssp-2.1.0 and I am getting that error you got: dssp cmd='/usr/local/bin/dssp/ -i ddQ3PqtX -o ddR1HavD /dev/null 2 /dev/null' Reading frame 0 time0.000 Back Off! I just backed up ddQ3PqtX to ./#ddQ3PqtX.1# --**- Program do_dssp, VERSION 4.6 Source code file: /usr/local/bin/gromacs-4.6/**src/tools/ gmx_do_dssp.c, line: 667 Fatal error: Failed to execute command: Try specifying your dssp version with the -ver option. How can I fix that? Thanks 2013/1/15 James Starlight jmsstarli...@gmail.com Justin, thanks both options works perfect. James 2013/1/15 Justin Lemkul jalem...@vt.edu: On 1/15/13 7:13 AM, James Starlight wrote: Justin, I want to obtain timescale on X as well as number of residues on Y on the xmp graph . By default that graph has not legend so it's hard to analyse it . The legends are printed in the .xvg header. I've never had a problem plotting its contents (though they are usually somewhat unclear when plotted together) with xmgrace -nxy scount.xvg By the way have you forced with some problems with dppc ? Simetimes I've obtain error like There are 286 residues in your selected group dssp cmd='/usr/local/bin/dssp -i dd42GVbd -o ddpu8ln2 /dev/ null 2 /dev/null' Reading frame 0 time0.000 Back Off! I just backed up dd42GVbd to ./#dd42GVbd.1 Fatal error: Failed to execute command: Try specifying your dssp version with the -ver option. and I dont know how to fix it. I'm using gromacs-4.6-beta 3 with dssp 2.0.3 Since dssp changed its command line options, Gromacs had to adapt as well. The error tells you to use the -ver option; you should do so. Version 2 should be the default, so check to make sure you're actually using that version and not the old dssp. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/ Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. * Can't post
Re: [gmx-users] Number of interactions per residue
Hi, With -r2 one can provide a second, larger, cutoff so that contact kinetics can be analyzed within the Luzar-Chandler framework that were designed for hbonds. What index groups did you use? Erik On Feb 18, 2013, at 6:04 PM, Kavyashree M wrote: Dear users, As Suggested by Erik, I used g_hbond with -contact to obtain a matrix of each contact as a function of time. I used the following command - g_hbond -f a.xtc -s a.tpr -contact -r2 0.5 -hbm m.xpm -b 4000 -e 4400 -hbn c.ndx I get only three contacts in the index file. The protein is a dimer of 474 residues (237 each). With a distance cut off of 0.5nm there should have been more number of contacts. And what is the difference in using -r only or -r2 only and combining -r and -r2? Thank you Kavya On Thu, Feb 14, 2013 at 3:40 PM, Kavyashree M hmkv...@gmail.com wrote: Thank you! On Thu, Feb 14, 2013 at 3:38 PM, Erik Marklund er...@xray.bmc.uu.sewrote: Perhaps g_hbond -contact will do what you want. Erik On Feb 14, 2013, at 10:42 AM, Kavyashree M wrote: Dear users, How can I get the number of interactions of each residue within a cut off as a function of time. just like g_saltbr writes with the option -sep. I tried using g_mdmat but it gives an average contact map. Thank you Kavya -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Number of interactions per residue
Perhaps g_hbond -contact will do what you want. Erik On Feb 14, 2013, at 10:42 AM, Kavyashree M wrote: Dear users, How can I get the number of interactions of each residue within a cut off as a function of time. just like g_saltbr writes with the option -sep. I tried using g_mdmat but it gives an average contact map. Thank you Kavya -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] different springs - WHAM
On Feb 14, 2013, at 2:01 PM, Justin Lemkul wrote: On 2/13/13 5:23 PM, Steven Neumann wrote: On Tue, Feb 12, 2013 at 5:01 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/12/13 9:57 AM, Steven Neumann wrote: On Tue, Feb 12, 2013 at 2:53 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/12/13 9:40 AM, Steven Neumann wrote: Dear Gmx Users, I know it is possible to combine windows with different spring constants into the one PMF curve using g_wham. Do I have to somehow tell g_wham that one or two windows have different spring constants? No, they are read from the .tpr files. For instance - I got the better histogram overlap with lower force constant in one window. When I replace this window into the window with the sring constant like all windwos (worse overlap) both PMF curves differ app. 2kcal/mol which is around 30% of the overall deltaG. Is there any error I should inroduce when one window differ in terms of k1? What does g_wham's error analysis suggest? -Justin In both PMF error estimate with bayesian bootstraping is app. 0.2 kcal/mol Seems like a good result, so what's the problem? -Justin That the better overlap of histograms produce worse deltaG comparing to experiment. With all the same spring constants I get the experimental value of deltaG but there is a poor overlap. There must be (somehow) a correction added to deltaG when introdcuing windows with different spring constants. The code and/or g_wham paper should address this. In principle, WHAM can be conducted with any assortment of spring constants you like. If you track down a bug or something, please report it on redmine.gromacs.org. I read (and hacked) g_wham not that long ago. If I recall correctly it reads the force constants from the tpr. In fact, without those it would not be able to use pullf files. A workaround of course would be to simply add another window (or windows) with the same original force constant that gives adequate sampling. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Need advice on appending aa residues to the sequence
Hi, I have used MacroMolecule Builder for similar things. Erik On Feb 13, 2013, at 4:41 AM, zugunder wrote: Hi, I am sorry if this topic is not relevant for GROMACS forum, but I hope someone has faced the same problem before and could give me some advice... I need to simulate a relatively short protein (170aa) in water. No structures are available for it, so I used a Modeller web server to get some. Unfortunately, they only provided me with several truncated structures (with relatively high scores though) of 40 and 130aa length. However, they do not overlap and the gap is 4aa long. While doing a research on the better way to stitch them I ran a couple of simulations of 2 most high scoring structures for a 130fragment (C-term) and one of them seems to fold relatively quickly. The problem now is that I can't find a way to append those 4 residues to either of the sequences and stitch them into one to simulate the complete thing. I found several references to DeepView software, but it does not seem to work in my hands (or probably I am missing something). So if someone has faced the same problem or has any ideas on how to do this kind of reconstruction of the sequence for further simulation, I'd really appreciate any tips, advice or other input. Thank you. -- View this message in context: http://gromacs.5086.n6.nabble.com/Need-advice-on-appending-aa-residues-to-the-sequence-tp5005489.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] installation
It shouldn't generate output. It will make your system find your gromacs installation, however. Try e.g. which mdrun. Erik On Feb 13, 2013, at 5:06 AM, David Sáez wrote: Thanks for your answer Justin. I followed your advice: When I type *$ source /usr/local/gromacs/bin/GMXRC* *$* Nothing happened, the prompt returns normally and no action is executed. Do you have any idea? On Tue, Feb 12, 2013 at 11:27 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/12/13 9:24 PM, David Sáez wrote: Hello everybody, I'm trying to install Gromacs 4.6 in my Ubuntu 12.04 laptop. As I am not a a skilled user, I tried the Quick and Dirty Installation, After following the instructions I obtained this message when trying to execute GMXRC: david@HAL-9000:~$ /usr/local/gromacs/bin/GMXRC /usr/local/gromacs/bin/GMXRC: line 34: return: can only `return' from a function or sourced script /usr/local/gromacs/bin/GMXRC: line 43: CSH:: command not found /usr/local/gromacs/bin/GMXRC.**csh: line 8: syntax error near unexpected token `setenv' /usr/local/gromacs/bin/GMXRC.**csh: line 8: `if (! $? LD_LIBRARY_PATH) setenv LD_LIBRARY_PATH ' Could someone give some help? Note the first error - you need to source the file. $ source /usr/local/gromacs/bin/GMXRC -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- David A. Sáez San Martín Químico-Farmacéutico Concepción, Chile -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Calculation of the Force on the center of bonds
Try virtual sites constructions. On Feb 11, 2013, at 6:01 PM, Rasoul Nasiri wrote: Dear All, I need to define interaction sites on the center of C-H bonds instead of nuclei of each atom. The main reason was that non-bonding parameters (sigma and epsilon) have been parametrized in these centers and those are only available for the center of C-H. So, I just wanted to know how calculation of force can be implemented by GROMACS in this case. Best wishes Rasoul -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] The time for the temperature and pressure coupling
Hi, Perhaps a side point: Temperature and pressure can not be seen as constraints to the system at any given instant in the sense that e.g. the instantaneous kinetic energy perfectly match the temperature at every time step just because you have a thermostat. Time and ensemble averages will, however, reflect the temperature and pressure coupling. Erik On Feb 6, 2013, at 11:28 PM, Bao Kai wrote: Dear Gromacs Team, I have a small question related to the scheme of the MD in Gromacs. When are the temperature and pressure constrains are enforced, before the update of the velocity and position or after? Thank you very much. Best Regards, Kai -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] RNA MD
I've never seen good parameters for nucleic acids. There might be such, but none that ship with gromacs as far as I know. Erik On Feb 7, 2013, at 4:25 AM, 김현식 wrote: Dear experts, Hello! Is it possible to run RNA md with GBSA? Thank you. bestKim. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Regarding manual velocity generation in simulation
On Feb 5, 2013, at 8:22 AM, bipin singh wrote: Hello All, Please let me know whether is it possible to manually assign the velocity for each atom in the simulation instead of generating through gen_vel option. If the preceision of a gro-file is sufficient you can use such for manually setting velocities of individual atoms. -- *--- Thanks and Regards, Bipin Singh* -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Dynamics of the salt-bridges
Hi, If you don't care about the exact distances, but rather the time the groups spend within a certain distance, g_hbond -contact can be useful. Best, Erik On Feb 3, 2013, at 6:36 PM, James Starlight wrote: Justin, 1 )for example I want to select in index file only all asp, glu and his residues ( I could find selection by residue type only). 2) Than I'd like that gromacs compute dynamics of the distance between that charge groups (providing only truncated .tpr file as the input) but only. Could other than g_saltbr gromacs tools be used for that (E,g g_dist ) ? James 2013/2/3 Justin Lemkul jalem...@vt.edu: On 2/3/13 1:01 AM, James Starlight wrote: Justin, thanks again for suggestions. I'm not quite sure how I can use tpbconv -zeroq. For example I want to reduce charges of all amino acids except Asp Glu and His ( to monitor s.b dynamics between that groups only). As I understood -zeroq working with the groups defined in the index file so I should just select all residues that I need in that file, shouldnt it ? Also doest it possible to select pairs of residues Yes. placed in the sequence on the distant sites ? (e.g by selecting only pairs within some range of n1 and n2+k where kn1+10) I don't understand what you mean. tpbconv will only take one index group for zeroing charges, so I don't understand how such a relative scheme would work for all cases. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] How to analysis 10 ns from 20 ns simulation
HI, It should read trjconv. And all analysis tools have the -b and -e flags for excluding the start or the end of a trajectory. Erik On Feb 4, 2013, at 7:00 AM, Emanuel Birru wrote: Use trajconv http://manual.gromacs.org/online/trjconv.html -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org ] On Behalf Of Naga Sundar Sent: Monday, 4 February 2013 4:45 PM To: Discussion list for GROMACS users Subject: [gmx-users] How to analysis 10 ns from 20 ns simulation Dear users I performed 20 ns simulation for protein complex. After 10 ns only my system obtained equilibration state . I would like to analyze last 10 ns from the trajectory file.I got problem to generate last 10 ns xtc file from the 20 ns trr file. so, plz help me to sort out this problem -- Regards N.NagaSundaram -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Visualize Protein ligand complex after simulation
Short answer is to inspect your complex with VMD or Pymol (or some other viewer). Pymol takes pdb input, so unless your structure is contained in a pdb file you must convert it with e.g. trjconv first. If you want a single frame you need to extract one form your trajectory, or, if the final frame form your simulation suffices, then use the -c output from mdrun. Most likely you will want to take care of the periodic boundary conditions, so a round of trjconv is probably needed anyway. Ask again or look at the gromacs mailing-list archive if there is anything specific that puzzles you. Erik On Jan 28, 2013, at 3:30 PM, Sainitin Donakonda wrote: Hello, Recently i started working on molecular dynamics on my protein ligand complex using gromacs i successfully did simulation but i dont know how to visualize this protein-ligand complex this after MD simulation Can any body tell me how to do it? Thanks Nitin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] RMSD
On Jan 25, 2013, at 5:53 AM, Shima Arasteh wrote: Thanks for your reply. I want to chose one of the 5 conformers from a NMR PDB. As I studied in literature, the average structure could be selected regarding RMSD values and the go on with selected one to simulate in in water, lipid bilayer. All right, I may make a matrix, but how would I chose my purposed conformers? Thanks for all your suggestions. Sincerely, Shima From: Leandro Bortot leandro@gmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thursday, January 24, 2013 8:54 PM Subject: Re: [gmx-users] RMSD you can make a simple script which calculates all the pairwise RMSD values with g_rms. By doing this you can make a RMSD matrix. I think you can get the RMSD matrix from g_cluster in one go. The usefulness of this depends on what you are trying to see, which wasn't clearly stated to us. I did it once because I wanted to know how similar the 20 conformers from a NMR PDB actually were. 2013/1/24 FLOR MARTINI flormart...@yahoo.com.ar The values are OK, you obtain a value of RMSD of 0.2510229 . The value -1 refers time, and it is because you do not have a trajectory. You are comparing only two .pdb structures, so it is consistent that you obtain only one value, as you do not have more than one frame to compare. Regards Flor Dra.M.Florencia Martini Cátedra de Farmacotecnia II Facultad de Farmacia y Bioquímica Universidad de Buenos Aires Junín 956 6º (1113) TE: 54 011 4964-8273 De: Shima Arasteh shima_arasteh2...@yahoo.com Para: Discussion list for GROMACS users gmx-users@gromacs.org Enviado: miércoles, 23 de enero de 2013 16:14 Asunto: Re: [gmx-users] RMSD What I see in xvg file is as below: # g_rms -s 1.pdb -f 2.pdb -o rmsd1.xvg # # g_rms is part of G R O M A C S: # # Gromacs Runs On Most of All Computer Systems # @title RMSD @xaxis label Time (ps) @yaxis label RMSD (nm) @TYPE xy @ subtitle Protein after lsq fit to Protein -1.0000.2510229 I though that -1 is the ref value and the other is the relative RMSD for 2.pdb. Is this -1 should be positive? What is this -1? Would you give me any suggestions please? Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Wednesday, January 23, 2013 9:36 PM Subject: Re: [gmx-users] RMSD On 1/23/13 12:48 PM, Shima Arasteh wrote: I want to find the structure with the lowest RMSD, so I think it does not make different to set any of pdb files as the ref structure. I made an attempt and got the RMSD regarding the first pdb file. The RMSD relative to -1 for the ref structure, is written in xvg file. Is my approach logically correct? The RMSD value should be positive, so I don't know how you get -1. Your approach does not seem very sound - a structure does not have an absolute RMSD value; it has an RMSD value relative to a reference structure, which must be some sort of meaningful comparison or else you're not really measuring anything useful. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read
Re: [gmx-users] Hydrogen bonding differences
There were a handful of bugfixes to g_hbond over the last year. Could you try 4.6 or a smoking hot 4.5.5? I recognize this discrepancy form before. Erik On Jan 24, 2013, at 3:59 PM, Kavyashree M wrote: Dear Sir, This is 4.5.3. I have not tried nomerge. I did not use nomerge option in any of them, So if it has counted it (Hbond b/w same donor and acceptor but with different hydrogen) twice in one calculation then it will be counted twice in another, So wont the result with/without nomerge be the same? The difference is 4-5 Hbonds.. Thank you Kavya On Thu, Jan 24, 2013 at 7:30 PM, Erik Marklund er...@xray.bmc.uu.se wrote: Hi. What version was this? Have you tried with -nomerge? Erik On Jan 21, 2013, at 10:55 AM, Kavyashree M wrote: Dear users, While calculating hydrogen bonds for a simulation, it was found that the average number of intra protein hbonds was not equal to sum of MM, MS and SS hydrogen bonds. (MM - main chain - main chain, MS - main chain - side chain and side chain - side chain hydrogen bonds). There was a difference of 5 or so hbonds between intra-protein and MM+MS+SS hbonds. why is this so? I selected the options 7 7 for MM, 7 8 for MS and 8 8 for SS hydrogen bonds. One clarification. nhbdist option gives 0, 1, 2, 3 and total hydrogen bonds per hydrogen. Does this mean that a single hydrogen involving in forming hbond with 2 different acceptors/donors at different points of time in the trajectory. Thanks kavya -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Hydrogen bonding differences
Hi. What version was this? Have you tried with -nomerge? Erik On Jan 21, 2013, at 10:55 AM, Kavyashree M wrote: Dear users, While calculating hydrogen bonds for a simulation, it was found that the average number of intra protein hbonds was not equal to sum of MM, MS and SS hydrogen bonds. (MM - main chain - main chain, MS - main chain - side chain and side chain - side chain hydrogen bonds). There was a difference of 5 or so hbonds between intra-protein and MM+MS+SS hbonds. why is this so? I selected the options 7 7 for MM, 7 8 for MS and 8 8 for SS hydrogen bonds. One clarification. nhbdist option gives 0, 1, 2, 3 and total hydrogen bonds per hydrogen. Does this mean that a single hydrogen involving in forming hbond with 2 different acceptors/donors at different points of time in the trajectory. Thanks kavya -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] how can I make statics for Z-axis?
g_traj -nox -noy if I recall correctly. On Jan 21, 2013, at 4:10 PM, Albert wrote: hello: I would like to make statics for an atom along Z-axis. I am just wondering how can I to do this in Gromacs? thank you very much best Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] mdp option for implicit solvent simulation
Hi, If you're simulating in the gas-phase, how come you want implicit solvent? Erik On Jan 11, 2013, at 5:07 AM, Sanku M wrote: Hi, I am trying to do implicit solvent simulation for a protein in gas- phase. I have a few questions : 1) should I use sd integrator? 2) should I also use no periodic condition considering continuum dielectric ? 3) in the JCTC 2010 paper by Lindahl and co-worker, it is mentioned that no cutoffs were used for implicit solvent simulations. But, again in implicit solvent setup the rgblist should be equal to rlist. Now, if I use rlist=0 ( as all interactions are considered), should I also make rgblist=0? Does it mean the setup was following type: i.e. ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 0 ; ns algorithm (simple or grid) ns-type = simple ; Periodic boundary conditions: xyz, no, xy pbc = no periodic_molecules = no ; nblist cut-off rlist= 0 ; long-range cut-off for switched potentials rlistlong= -1 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = cut-off rcoulomb-switch = 0 rcoulomb = 0 ; Relative dielectric constant for the medium and the reaction field epsilon_r= 1 epsilon_rf = 1 ; Method for doing Van der Waals ; Method for doing Van der Waals vdw-type = Cut-off ; cut-off lengths rvdw-switch = 0 rvdw = 0 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = No ; IMPLICIT SOLVENT ALGORITHM implicit_solvent = GBSA ; GENERALIZED BORN ELECTROSTATICS ; Algorithm for calculating Born radii gb_algorithm = Still ; Frequency of calculating the Born radii inside rlist nstgbradii = 1 ; Cutoff for Born radii calculation; the contribution from atoms ; between rlist and rgbradii is updated every nstlist steps rgbradii = 0 ; Dielectric coefficient of the implicit solvent gb_epsilon_solvent = 80 ; Salt concentration in M for Generalized Born models gb_saltconc = 0.150 ; Scaling factors used in the OBC GB model. Default values are OBC(II) gb_obc_alpha = 1 gb_obc_beta = 0.8 gb_obc_gamma = 4.85 gb_dielectric_offset = 0.009 sa_algorithm = Ace-approximation sa_surface_tension = -1 Some idea about the implicit solvent setup will be appreciated. Sanku -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] using g_analyze for calculating distance autocorrelation functions
It is common to subtract the average value of the data. Hence the ACF usually contain negative values. 20 dec 2012 kl. 14.30 skrev 申昊: Dear GROMACS users, I have been working on calculating distance autocorrelation functions by using g_analyze. The codes i used was g_analyze -f dist.xvg -ac autocorr.xvg -temp 300. 'dist.xvg' is about the average distance against simulation time. The two columns are both positive datas. However, the result show a mixture of positive and negative datas. In my opinion, the autocorrelation function should be always positive. Can anyone help me with that ? HaoShen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] merge .gro, .top files
18 dec 2012 kl. 09.30 skrev Tsjerk Wassenaar: Hi KT, If you mean concatenating frames in .gro files, you can use trjcat or just cat. If you mean merging the coordinates, it's a wee bit more complicated. Since you also ask for top files, I guess that's the case. Here's a snippet of python code that will do the trick: #!/usr/bin/env python import sys f = [open(i).readlines() for i in sys.argv[1:]] print Merged gro file\n%5d % (sum([len(i) for i in f]) - 3*len(f)) print .join([.join(i[2:-1]) for i in f]), print f[0][-1] For the top files, it is necessary to ensure all the moleculetypes are #included, and that the [ molecules ] listing under [ system ] has the right number and order of the molecules in the merged gro file. There's no tool for that that I know of. In principle you could use grompp for checking that. It would print out a heap of warinngs/notes/errors if structure file and topology don't match. Erik Cheers, Tsjerk On Tue, Dec 18, 2012 at 6:18 AM, Kieu Thu Nguyen kieuthu2...@gmail.comwrote: Dear All, I don't know which tools used to merge 2 files .gro, 2 files .top ? Can i use trjcat ? Thanks ! KT -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Biocomputing Group Department of Biological Sciences 2500 University Drive NW Calgary, AB T2N 1N4 Canada -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Asymmetry in homo dimer simulation
5 dec 2012 kl. 17.26 skrev Justin Lemkul: On 12/5/12 11:21 AM, Kavyashree M wrote: Sir, Thank you for your suggestions. I decided the cutoff based on RMSD convergence. I will calculate at different time intervals. Running multiple simulation is definitely the best suggestion but due to time and machine constraint it would be difficult. Instead I have two mesophilic simulations. But Is there any other way by which I can prove this point? Not using single trajectories. Your job is to convince reviewers that your work is sound. A single trajectory is not convincing, at least to any reviewer that does his or her homework :) I don't think that the use of single trajectories is necessarily wrong, as long as they are sufficiently long. It's usually the amount of sampling that is the crucial point, no? Erik -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Observations about g_hbond -dist and -ang
30 nov 2012 kl. 12.24 skrev Cara Kreck: Hi everyone, Ithought I should share something that I've noticed about some of the outputs of g_hbond, in case it's confused anyone else. I'd noticed that there is a significant difference in the length distribution plots (-dist) produced by version 3.3.3 and all of the 4 family, including 4.5.5 (which I believe included a bugfix for g_hbond). I then figured out that this difference is really just a problem with the .xvg legends. In 3.3.3 the distribution values were calculated for Hydrogen - Acceptor Distance (nm) and this description is still provided in the legend for 4.5.5, even though the values provided now are actually Donor - Acceptor Distance (nm). If you use -noda in 4.5.5 it will give you an identical distribution to 3.3.3. I then realised that both versions also have the angle distribution plots (-ang) labelled wrongly with Donor - Hydrogen - Acceptor Angle (\SO\N) instead of Hydrogen - Donor - Acceptor Angle. I'm not sure if these things would really be considered bugs, but I just thought I'd let people know. Thanks for pointing it out. I'd call it a bug, but a low priority one. Would you mind filing a redmine issue about it (http://redmine.gromacs.org/projects/gromacs/issues)? Then this will be much less likely to be overlooked or forgotten about. Erik Cara -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Hbonds between Adenine and Thymine
Hi, A general note: make_ndx and index files are not magical in any way. You can usually construct an index group from e.g. a pdb file with awk. It's just lists of atom indices. Best, Erik 28 nov 2012 kl. 22.33 skrev Justin Lemkul: On 11/28/12 3:43 PM, Hovakim Grabski wrote: Dear Gromacs users, I set a simulation of 26 base pairs of DNA with Ethidium Bromide for 5 ns. After a while Thymine rotated for about 70 degrees and then returned to its initial position. I wanted to find out hbonds between Adenine and Thymine but with make_ndx things don't work so well. How can I select Adenine from one strand and Thymine from the other strand and then run g_hbond ? You can use make_ndx to select any residues you want. You'll have to describe exactly what you did that produced insufficient results. Saying it didn't work well doesn't tell us anything, because it is in fact quite easy to produce usable index groups. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] how to repeat simulation correctly?
Stochastic and chaotic are not identical. Chaotic means that differences in the initial state will grow exponentially over time. Erik 22 nov 2012 kl. 09.52 skrev Felipe Pineda, PhD: Won't this same stochastic nature of MD provide for different, independent trajectories even if restarted from a previous, equilibrated frame even without resetting velocities, i.e., as a continuation run using the velocities recorded in the gro file of the selected snapshot? Felipe On 11/22/2012 12:55 AM, Mark Abraham wrote: Generating velocities from a new random seed is normally regarded as good enough. By the time you equilibrate, the chaotic nature of MD starts to work for you. Mark On Nov 21, 2012 1:04 PM, Felipe Pineda, PhD luis.pinedadecas...@lnu.se wrote: So how would you repeat the (let be it converged) simulation from different starting conditions in order to add that valuable statistics you mention? I think this was Albert's question Felipe On 11/21/2012 12:41 PM, Mark Abraham wrote: If a simulation ensemble doesn't converge reliably over a given time scale, then it's not converged over that time scale. Repeating it from different starting conditions still adds valuable statistics, but can't be a replicate. Independent replicated observations of the same phenomenon allow you to assess how likely it is that your set of observations reflect the underlying phenomenon. The problem in sampling-dependent MD is usually in making an observation (equating a converged simulation with an observation). Mark On Wed, Nov 21, 2012 at 8:12 AM, Albert mailmd2...@gmail.com wrote: hello: I am quite confused on how to repeat our MD in Gromacs. If we started from the same equilibrated .gro file with gen_vel= no in md.mdp, we may get exactly the same results which cannot be treated as reasonable repeated running. However, if we use gen_vel=yes for each round of running, sometimes our simulation may not converged at our simulated time scale and we may get two results with large differences. So I am just wondering how to perform repeated MD in Gromacs in a correct way so that our results can be acceptably repeated? thank you very much. Albert -- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] how to repeat simulation correctly?
It will depend on the integration algorithms, parallelization, etc. The equations are deterministic, but numerical differences may arise e.g. from different ordering of floating point numbers being added together in different simulations. The chaotic nature of MD would then have the simulations diverge over time, but the question is how long it takes for such differences to really manifest. Best, Erik 22 nov 2012 kl. 10.13 skrev Felipe Pineda, PhD: Would non-deterministic be correct to characterize the nature of MD as well? There is also deterministic chaos ... And what about the outcome of starting several trajectories from the same equilibrated frame as continuation runs, i.e., using its velocities? Could they be considered independent and used to extract that valuable statistics mentioned in a previous posting? Felipe On 11/22/2012 10:04 AM, Erik Marklund wrote: Stochastic and chaotic are not identical. Chaotic means that differences in the initial state will grow exponentially over time. Erik 22 nov 2012 kl. 09.52 skrev Felipe Pineda, PhD: Won't this same stochastic nature of MD provide for different, independent trajectories even if restarted from a previous, equilibrated frame even without resetting velocities, i.e., as a continuation run using the velocities recorded in the gro file of the selected snapshot? Felipe On 11/22/2012 12:55 AM, Mark Abraham wrote: Generating velocities from a new random seed is normally regarded as good enough. By the time you equilibrate, the chaotic nature of MD starts to work for you. Mark On Nov 21, 2012 1:04 PM, Felipe Pineda, PhD luis.pinedadecas...@lnu.se wrote: So how would you repeat the (let be it converged) simulation from different starting conditions in order to add that valuable statistics you mention? I think this was Albert's question Felipe On 11/21/2012 12:41 PM, Mark Abraham wrote: If a simulation ensemble doesn't converge reliably over a given time scale, then it's not converged over that time scale. Repeating it from different starting conditions still adds valuable statistics, but can't be a replicate. Independent replicated observations of the same phenomenon allow you to assess how likely it is that your set of observations reflect the underlying phenomenon. The problem in sampling-dependent MD is usually in making an observation (equating a converged simulation with an observation). Mark On Wed, Nov 21, 2012 at 8:12 AM, Albert mailmd2...@gmail.com wrote: hello: I am quite confused on how to repeat our MD in Gromacs. If we started from the same equilibrated .gro file with gen_vel= no in md.mdp, we may get exactly the same results which cannot be treated as reasonable repeated running. However, if we use gen_vel=yes for each round of running, sometimes our simulation may not converged at our simulated time scale and we may get two results with large differences. So I am just wondering how to perform repeated MD in Gromacs in a correct way so that our results can be acceptably repeated? thank you very much. Albert -- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] how to repeat simulation correctly?
MD is chaotic regardless of how differences, however small, are created in the first place. This was just one example. Stochastic terms in e.g. the v-rescale thermostat will rely on the same sequence of random numbers in separate simulations if the random number generator is seeded in the same way. But sure, choosing different seeds would be one way of having diverging simulations. I think your point is correct in principle, e.g. when pressure is concerned. That equilibration time must however also be put in relation to how long it takes for two simulations to become uncorrelated. Best, Erik 22 nov 2012 kl. 11.30 skrev Felipe Pineda, PhD: Not to forget about the additional stochastic term in the V-rescale thermostat, when it's used. Since the equations are evidently deterministic, is the chaotic nature of MD just a numerical effect? The practical point: if the velocities are reset upon a restart from an equilibrated frame in order to generate multiple, independent trajectories for statistical purposes, the equilibration will be probably lost and a new equilibration phase will be needed. Is this correct? Best, Felipe On 11/22/2012 11:12 AM, Erik Marklund wrote: It will depend on the integration algorithms, parallelization, etc. The equations are deterministic, but numerical differences may arise e.g. from different ordering of floating point numbers being added together in different simulations. The chaotic nature of MD would then have the simulations diverge over time, but the question is how long it takes for such differences to really manifest. Best, Erik 22 nov 2012 kl. 10.13 skrev Felipe Pineda, PhD: Would non-deterministic be correct to characterize the nature of MD as well? There is also deterministic chaos ... And what about the outcome of starting several trajectories from the same equilibrated frame as continuation runs, i.e., using its velocities? Could they be considered independent and used to extract that valuable statistics mentioned in a previous posting? Felipe On 11/22/2012 10:04 AM, Erik Marklund wrote: Stochastic and chaotic are not identical. Chaotic means that differences in the initial state will grow exponentially over time. Erik 22 nov 2012 kl. 09.52 skrev Felipe Pineda, PhD: Won't this same stochastic nature of MD provide for different, independent trajectories even if restarted from a previous, equilibrated frame even without resetting velocities, i.e., as a continuation run using the velocities recorded in the gro file of the selected snapshot? Felipe On 11/22/2012 12:55 AM, Mark Abraham wrote: Generating velocities from a new random seed is normally regarded as good enough. By the time you equilibrate, the chaotic nature of MD starts to work for you. Mark On Nov 21, 2012 1:04 PM, Felipe Pineda, PhD luis.pinedadecas...@lnu.se wrote: So how would you repeat the (let be it converged) simulation from different starting conditions in order to add that valuable statistics you mention? I think this was Albert's question Felipe On 11/21/2012 12:41 PM, Mark Abraham wrote: If a simulation ensemble doesn't converge reliably over a given time scale, then it's not converged over that time scale. Repeating it from different starting conditions still adds valuable statistics, but can't be a replicate. Independent replicated observations of the same phenomenon allow you to assess how likely it is that your set of observations reflect the underlying phenomenon. The problem in sampling-dependent MD is usually in making an observation (equating a converged simulation with an observation). Mark On Wed, Nov 21, 2012 at 8:12 AM, Albert mailmd2...@gmail.com wrote: hello: I am quite confused on how to repeat our MD in Gromacs. If we started from the same equilibrated .gro file with gen_vel= no in md.mdp, we may get exactly the same results which cannot be treated as reasonable repeated running. However, if we use gen_vel=yes for each round of running, sometimes our simulation may not converged at our simulated time scale and we may get two results with large differences. So I am just wondering how to perform repeated MD in Gromacs in a correct way so that our results can be acceptably repeated? thank you very much. Albert -- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688
Re: [gmx-users] Save frames of trajectory file
trjconv 19 nov 2012 kl. 10.47 skrev Shima Arasteh: Dear gmx users, Is there any command in GROMACS, which I can use it to save frames of trajectory file in pdb format? Sincerely, Shima -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Force vs distance plot in pulling simulation?
16 nov 2012 kl. 22.42 skrev Justin Lemkul: On 11/16/12 10:45 AM, Gmx QA wrote: Hello gmx-users, I've performed a pulling simulation and obtained a force-vs-time plot and a distance-vs-time plot (xvg-files). Is it common to somehow combine these to get a force-vs-distance-plot using a hacked-together script, or how do people that have experience with pulling generally make such a plot? I have read a bunch of papers where such figures are presented, but there does not seem to be any built-in way in gromacs to make them. I could be wrong, of course. The only solution is to write a simple script that parses out the columns you want. -Justin I don't see the point though. Except for checking implementation of the pull code. --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Umbrella sampling question
Hi, Blindly defining the center of mass for a group of atoms is not possible in a periodic system such as a typical simulation box. You need some clue as to which periodic copy of every atom that is to be chosen. By providing pull_pbcatom0 you tell gromacs to, for every atom in grp0, use the periodic copy closest to the atom given by pull_pbcatom0. If you have large pullgroups this is necessary to define the inter-group distance in a way that makes sense. If you get different results depending on that setting you really need to figure out which atom is a good center for your calculations. The default behavior is to use the atom whose *index* is in the center of the group. If you for example have a dimeric protein this may correspond to the C-terminus of the first chain or the N-terminus of the second one, which in turn often doesn't coincide with the geometrical center of the group. I suggest you try yet another choice of pull_pbcatom0 that is also close to the center to see if that also give rise to a different distance. As mentioned, the choice of pull_pbcatom0 should not matter as long as the choice allows to figure out how to handle the periodicity. Best, Erik 15 nov 2012 kl. 19.56 skrev Gmx QA: Hi Chris Seems my confusion was that I assumed that the distances in the profile.xvg-file should correspond to something I could measure with g_dist. Turns out it does not. Thank you for helping me sorting out this, I got it now :-) About pull_pbcatom0 though. My box is 2*1.08 nm in all directions: $ tail -n 1 conf0.gro 12.45770 12.45770 17.99590 I am still not sure what pull_pbcatom0 does. You said it should not have any effect on my results, but changing it does result in a different initial distance reported by grompp. In my initial attempts at this, I did not specify anything for pull_pbcatom0, but in the grompp output I get this Pull group natoms pbc atom distance at start reference at t=0 0 21939 10970 1 1 0 2.083 2.083 Estimate for the relative computational load of the PME mesh part: 0.10 This run will generate roughly 761 Mb of data Then, following the advice in the thread I referred to earlier, I set pull_pbcatom0 explicitly in the mdp-file to be an atom close to the COM of the Protein. Then I get from grompp Pull group natoms pbc atom distance at start reference at t=0 0 21939 7058 1 1 0 1.808 1.808 Estimate for the relative computational load of the PME mesh part: 0.10 This run will generate roughly 761 Mb of data As you can see, the initial distance is different (2.083 vs 1.808), and 1.808 is the same as the distance reported by g_dist. Do you have any comments here as to why this is? Thanks /PK What you reported is not what you did. It appears that grompp, gtraj, and g_dist report the same value. Please also report the value that you get from your pullx.xvg file that you get from mdrun, which I suspect will also be the same. The difference that you report is actually between the first FRAME of your trajectory from g_dist and the first LINE of the file from the g_wham output. I see no reason to assume that the values in the output of g_wham must be time-ordered. Also, I have never used g_wham myself (I use an external program to do wham) and so I can not say if you are using it correctly. My overall conclusion is that you need to investigate g_wham output not worry about a new run at this stage. Regarding pull_pbcatom0, there is lots of information on the mailing list about this. It is a global atom number that defines the unit cell for selection of which periodic image of each molecule will be used for the pulling. If all of your box dimensions are 2*1.08 nm, then pull_pbcatom0 will not affect your results. Chris. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support
Re: [gmx-users] Dihedral form
You could shift the reference angle by pi, which changes the sign of the cosine.
Best,
Erik
15 nov 2012 kl. 14.25 skrev Laura Leay:
All,
I would like to parameterise the Dreiding force field for use with Gromacs.
One thing I am not sure about is how to parameterise the dihedrals
The Dreiding paper has the form;
E= 0.5k { 1 - cos[ n( phi - phi_o)]}
However I cannot find this form in the Gromacs manual. The closest I can find
in the Gromacs manual is:
E = k [ 1 + cos(n*phi - phi_s) ]
Does anyone know of a way to use the Dreiding form in Gromacs, or to convert
to a form that is more suitable for use with Gromacs?
Many thanks,
Laura
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Re: [gmx-users] Dihedral form
Hi,
15 nov 2012 kl. 15.41 skrev Laura Leay:
Thanks Eric,
Just to clarify (I hope this notation is in fact clear):
E=0.5k [ 1 - cos( n*phi - n*phi_o +180 ) ] = 0.5k [ 1 + cos(n*phi - n*phi_o)]
^ this whole equation is Dreiding ^this whole equation is
Dreiding converted to the form in Gromacs
This would mean that:
0.5k in Dreiding = k in Gromacs
n in Dreiding = n in Gromacs
n*phi_o +180 in Dreiding (original form) is phi_s in the Gromacs notation
from the original post
I think that's correct.
I hope this makes sense!
Laura
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Erik Marklund [er...@xray.bmc.uu.se]
Sent: 15 November 2012 13:37
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Dihedral form
You could shift the reference angle by pi, which changes the sign of the
cosine.
Best,
Erik
15 nov 2012 kl. 14.25 skrev Laura Leay:
All,
I would like to parameterise the Dreiding force field for use with Gromacs.
One thing I am not sure about is how to parameterise the dihedrals
The Dreiding paper has the form;
E= 0.5k { 1 - cos[ n( phi - phi_o)]}
However I cannot find this form in the Gromacs manual. The closest I can
find in the Gromacs manual is:
E = k [ 1 + cos(n*phi - phi_s) ]
Does anyone know of a way to use the Dreiding form in Gromacs, or to convert
to a form that is more suitable for use with Gromacs?
Many thanks,
Laura
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Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 6688fax: +46 18 511 755
er...@xray.bmc.uu.se
http://www2.icm.uu.se/molbio/elflab/index.html
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er...@xray.bmc.uu.se
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Re: [gmx-users] amino acid color
Hi, If you put the hydrophobicity in the b-factor column of a pdb file then pymol can use it for coloring. Best, Erik 14 nov 2012 kl. 14.14 skrev tarak karmakar: Dear All, In the active site cavity there are hydrophobic and hydrophilic amino acid residues. Now I want to provide color according to the hydrophobicity of the amino acids present thereby, suppose the color will start from BLUE (for the most hydrophobic) to RED ( most hydrophilic). Could anyone suggest me any software to make this type of picture ? Thanks -- Tarak -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Umbrella sampling question
pull the pg1-molecule straight up in z, and that is indeed also what is happening in the simulation. I ran this simulation for 6 ns, and it resulted in about 40 separate conformations to use for umbrella sampling. All of those simulations also seem to work, I can use the resulting pullf,xvg-files as input to g_wham, and get a histogram-plot with reasonable overlaps. However, I'm trying to understand how the various distances relate to each other. For example, in the profile.xvg-file I get a z-distance for the first frame as 1.761971 nm, while checking with g_dist gives me 1.80833 (for z). Continuing a few frames further, there are still differences, and they appear to be random. How are the distances in the profile.xvg-file computed? The average of the dZ column of the pullx-file for the first frame is 1.75787, which is sort of close to 1.761971, but not quite (and also for the next frames there is no closeness). Sorry if this became a long mail, but I need to understand this in order to be able to progress with my research. Thanks -- Message: 5 Date: Tue, 13 Nov 2012 16:54:47 -0500 From: Justin Lemkul jalem...@vt.edu Subject: Re: [gmx-users] Re: Diatomic in MeCN NPT (NH and PR) simulation segfaults after 1 us To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 50a2c1a7.7050...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 11/13/12 2:56 PM, benjfitz wrote: Are there any other tests I should run to diagnose the problem? I doubt there's anything that can be done that will be particularly useful. You could compile in debugging mode and try to do a backtrace when the problem occurs, but if you have a means to run stable simulations (500-ns intervals), I don't know whether that's worth it to you or not. I doubt any of the developers are going to want to run microsecond simulations to try to track it down. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- Message: 6 Date: Tue, 13 Nov 2012 23:27:28 -0800 (PST) From: Raj princecrusia...@gmail.com Subject: [gmx-users] Re: hydrophobic contacts To: gmx-users@gromacs.org Message-ID: 1352878048599-5002931.p...@n6.nabble.com Content-Type: text/plain; charset=us-ascii Hi all, can some one tel me how can i prepare a index file specifying the hydrophobic atoms along for measuring the hydrophobic contacts in the systems alone. -- View this message in context: http://gromacs.5086.n6.nabble.com/hydrophobic-contacts-tp4998153p5002931.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! End of gmx-users Digest, Vol 103, Issue 61 ** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] calculating lennard-jones interaction
Hi, Could you rephrase the question? Distance larger than cut-off and cut-off is less than distance seem equal by definition to me. Best, Erik 13 nov 2012 kl. 10.50 skrev Zahra M: hi dear users wanna know if the distance between two species is more than the cut off radius of vdw interaction (in a SMD simulation), can we trust the simulation results? I mean what is the difference between this case and the situation that the cut off radius is lower than the distance between two species. bests. Zahra -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] calculating lennard-jones interaction
Hi, There is a net attractive force from vdw interactions beyond the cut-off, which can be corrected for analytically *in the case of a homogeneous system*. There is a slight artifact arising from the use of cut-offs for non-homogeneous systems such as a protein in water. Often the same corrections are used for non-homogeneous systems. It all boils down to what you want to measure, if those artifacts are large enough to ruin your investigations. 13 nov 2012 kl. 17.46 skrev Zahra M: thank you for your reply I mean the distance between two proteins is more than the cut off value, and in the other case the distance between two proteins is less than the cut off value, Bests -Zahra From: Erik Marklund er...@xray.bmc.uu.se To: Zahra M s_zahra_mous...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Tuesday, November 13, 2012 2:08 PM Subject: Re: [gmx-users] calculating lennard-jones interaction Hi, Could you rephrase the question? Distance larger than cut-off and cut-off is less than distance seem equal by definition to me. Best, Erik 13 nov 2012 kl. 10.50 skrev Zahra M: hi dear users wanna know if the distance between two species is more than the cut off radius of vdw interaction (in a SMD simulation), can we trust the simulation results? I mean what is the difference between this case and the situation that the cut off radius is lower than the distance between two species. bests. Zahra -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] do_dssp Segmentation fault
Hi, The explanation is that DSSP changed its syntax some time ago and do_dssp no longer complied. More recent versions of do_dssp follows the new syntax while still supporting the old one. Erik 12 nov 2012 kl. 10.55 skrev João Henriques: Hello, do_dssp (4.5.5) is broken. There are two possible answers you're gonna get here: 1) Use old dssp, which you are using. 2) You're an idiot, which are not. What I did to solve the problem was, download gmx from git, and substitute the /src/tools/do_dssp.c of gmx 4.5.5 with the one from the git version. Re-compile it and voila! This do_dssp version accepts both old and new dssp and you have to specify which version with the flag -ver if I remember correctly. This worked perfectly for me. I hope it helps you as well. All the best, João Henriques On Mon, Nov 12, 2012 at 8:38 AM, mshappy1986 mshappy1...@126.com wrote: Hi all, I am meeting the following error in Gromacs 4.5.5 with do_dssp Here is the command do_dssp -f md.xtc -s md.tpr -o dssp.xpm give me the following error segmentation fault I have downloaded the executable DSSP form http://swift.cmbi.ru.nl/gv/dssp/ and set the environment variable, but do_dssp did not work. How can I fix it? Thanks a lot -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- João Henriques -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] problem with simulation of freezing of water
The phase transition of water from liquid to ice is very hard to observe in MD simulations. In the lab you can in fact supercool water for minutes without ice forming until you trigger the phase transition by e.g. knocking the beaker or add nucleating agents. An MD simulation takes place on timescales that are many orders of magnitude shorter, so obtaining ice in simulations when starting form a liquid system seem as likely as winning a billion dollars and getting struck by lightning at the same time. There are water models that nucleate much more easy than in experiments, which may be useful for you. Best, Erik 11 nov 2012 kl. 15.53 skrev Ali Alizadeh: Dear All users I did simulation of water freezind at low temperature(260 k) so that i was hoped to see regular structure of ice, I used OPLS-AA force field, SPC and 100ns, But i can not see the regular structure of ice(i used vmd for representation of my simulation)? In your opinion, Where did i mistake in my simulation? Where did i mistake in my simulation? -- Sincerely Ali Alizadeh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Running Gromacs in Clusters
Hi, I see degrading scaling when going from 96 to 192 cores on a cray for my system. I have periodic molecules and do umbrella sampling (with small deviations from the reference) which might affect the performance. My code is based on 4.5.5 without performance-critical modifications. Erik 9 nov 2012 kl. 03.06 skrev Szilárd Páll: Hi, With a fast network like Cray's you can easily get to 400-500 atoms/core core with 4.5 (that's 400+ cores for your system), perhaps even further. With 4.6 this improves quite a bit (up to 2-3x). -- Szilárd On Wed, Nov 7, 2012 at 5:19 PM, Erik Marklund er...@xray.bmc.uu.se wrote: Hi, Sure you can go beyond 24 cores. I'm currently simulating ~170 000 atoms on 192 cores at ~45 ns a day. with half the number of processors I get ~27 ns a day. It will of course depend on the hardware, particular algorithms, run parameters, and on the system details. Erik 7 nov 2012 kl. 16.51 skrev Marcelo Depolo: Good afternoon, I wonder if anyone has experience running Gromacs in MPI. I'm paralleling the processes and want to know how many processors reduces the computation time to the minimum. I am currently using 24 processors for a system of 170 000 atoms and obtaining a simulation of 50ns in 15 days. There's a way to reduce more this computational time? Thanks in advance! -- Marcelo Depólo Polêto Departamento de Bioquímica e Biologia Molecular Universidade Federal de Viçosa - UFV *Website: http://opensourcebioinformatics.com/site/* -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
