Re: [gmx-users] Pressure annealing in Gromacs?

On Thu, 2009-12-03 at 02:30 +1100, Mark Abraham wrote: > Jussi Lehtola wrote: > > I'm experiencing trouble converging the density of some heavy liquid > > alcohols (after 10 ns of simulation the density is still changing > > linearly). Is there any way to run pressure annealing in Gromacs? > > Run

Re: [gmx-users] Re:gmx-users Digest, Vol 67, Issue 150 (memory allocationerror)

hai justin, ya its robust. and urs is the only tutorial which i found for transmembrane protein MD simulation in GROMACS. Its really useful. thank you.As you said i tried it in other system also there i used gromacs version 3.3.3. i am getting the same kind of error.I didnt use any special conf

Re: [gmx-users] Re:gmx-users Digest, Vol 67, Issue 150 (memory allocationerror)

hai justin, ya its robust. and urs is the only tutorial which i found for transmembrane protein MD simulation in GROMACS. Its really useful. thank you.As you said i tried it in other system also there i used gromacs version 3.3.3. i am getting the same kind of error.I didnt use any special conf

Re: [gmx-users] RE: Mark & Justin - grompp error for gmxtest-4.0.4 and 3.3.3 on new gromacs-4.0.5 install

Yirdaw, Robel Birru wrote: Thank you both for your reply. So how did you guys verify and test gromacs on your machines? Mark, from your response, test-set 4.0.4 is of no use?! I have seen your other posts but the problem here is far more basic than that. It is of some use, but it is not robus

[gmx-users] program to look at the coordination number

You did not state clearly what you want to do. In many cases you could simply calculate the RDF using g_rdf and integrate to the first minimum. If that doesn't suit you, here's another idea: 1) g_rdf -> locate the first minimum 2) g_dist -dist to "print all the atoms in group 2 that are close

[gmx-users] program to look at the coordination number

Hai All Did anyone know a program to look at the coordination number for molecules??? Thanks... IMA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please

[gmx-users] PMF calculation using g_wham using different simulation boxes

Sorry, I don't use gromacs g_wham so I can't help you on the specifics there. I don't know if the -zprof0 does anything special, but you know that your PMF can be arbitrarily translated as dG is unknown to an additive constant, right? ## assume rx coord in first column and dG in second colu

[gmx-users] Re: PMF calculation using g_wham using different simulation boxes

Hi   Thank you Justin and Chris, for your comments and suggestions.   All the restrained distances are less than half of the box length. The reason I want to use different box sizes is:  g_wham gives zero value for the first bin, so I need extend my simulation for long restrant distances for th

Re: [gmx-users] How to plot Pressure (bar) vs simulation time in ps

Justin A. Lemkul wrote: Lum Nforbi wrote: Hi everyone, I need to plot a graph of pressure (bar) vs run time (ps) but I am havin problems with this because the graph's y-axis diplays energy (KJmol^-1) instead of pressure. How can I correct this energy on the y-axiz of my plot to pressure (b

Re: [gmx-users] How to plot Pressure (bar) vs simulation time in ps

Lum Nforbi wrote: Hi everyone, I need to plot a graph of pressure (bar) vs run time (ps) but I am havin problems with this because the graph's y-axis diplays energy (KJmol^-1) instead of pressure. How can I correct this energy on the y-axiz of my plot to pressure (bar)? Pressure is in bar

[gmx-users] How to plot Pressure (bar) vs simulation time in ps

Hi everyone, I need to plot a graph of pressure (bar) vs run time (ps) but I am havin problems with this because the graph's y-axis diplays energy (KJmol^-1) instead of pressure. How can I correct this energy on the y-axiz of my plot to pressure (bar)? I have used this command to view the value o

Re: SV: SV: SV: [gmx-users] g_saltbr

Hi Sarah, You may file the bug report. You can submit a small part of the trajectory to reproduce the error :) Cheers, Tsjerk On Wed, Dec 2, 2009 at 10:11 PM, Sarah Witzke wrote: > Hi Tsjerk and others, > > This is a very good explanation! Thank you. Did you mean I should file a bug > report

Re: [gmx-users] RE: Mark & Justin - grompp error for gmxtest-4.0.4 and 3.3.3 on new gromacs-4.0.5 install

Yirdaw, Robel Birru wrote: Thank you both for your reply. So how did you guys verify and test gromacs on your machines? Mark, from your response, test-set 4.0.4 is of no use?! I have seen your other posts but the problem here is far more basic than that. If it happens that 4.0.4 is usable to

SV: SV: SV: SV: [gmx-users] g_saltbr

Hi Tsjerk and others, This is a very good explanation! Thank you. Did you mean I should file a bug report or are you doing it since you understand the code? Thank you all! Sarah Fra: gmx-users-boun...@gromacs.org på vegne af Tsjerk Wassenaar Sendt: on 02-12-

[gmx-users] RE: Mark & Justin - grompp error for gmxtest-4.0.4 and 3.3.3 on new gromacs-4.0.5 install

Thank you both for your reply. So how did you guys verify and test gromacs on your machines? Mark, from your response, test-set 4.0.4 is of no use?! I have seen your other posts but the problem here is far more basic than that. If it happens that 4.0.4 is usable to some degree, there's still th

SV: SV: SV: SV: [gmx-users] g_saltbr

Sarah Witzke wrote: > In each of the files are a set of distances as a function of time - it does > not seem that strange, that the size is equal then. > > When I plot for instance the four .xvg files mentioned above I get four > different curves. Also "diff" lists that every line is differe

Re: [gmx-users] doing averages using g_angle

Hi Justin, Yes I understand what you are saying. Thank you amit On Wed, Dec 2, 2009 at 12:50 PM, Justin A. Lemkul wrote: > > > Amit Choubey wrote: > > >> >> On Wed, Dec 2, 2009 at 12:07 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote: >> >> >> >>Amit Choubey wrote: >> >>Hi Mark, >>

Re: [gmx-users] doing averages using g_angle

Amit Choubey wrote: On Wed, Dec 2, 2009 at 12:07 PM, Justin A. Lemkul > wrote: Amit Choubey wrote: Hi Mark, That is true. But what does the manual refer to when it says the first graph is the average, the rest are the individual angles

Re: [gmx-users] doing averages using g_angle

On Wed, Dec 2, 2009 at 12:07 PM, Justin A. Lemkul wrote: > > > Amit Choubey wrote: > >> Hi Mark, >> >> That is true. But what does the manual refer to when it says >> the first graph is the average, the rest are the individual angles >> >> what and where are the rest? I am only curious because th

Re: [gmx-users] doing averages using g_angle

Amit Choubey wrote: Hi Mark, That is true. But what does the manual refer to when it says the first graph is the average, the rest are the individual angles what and where are the rest? I am only curious because there might be a hidden feature that could be useful for me. Read all of

Re: [gmx-users] doing averages using g_angle

Hi Mark, That is true. But what does the manual refer to when it says the first graph is the average, the rest are the individual angles what and where are the rest? I am only curious because there might be a hidden feature that could be useful for me. Amit On Wed, Dec 2, 2009 at 12:21 AM, Mar

Re: SV: SV: SV: [gmx-users] g_saltbr

Hi, Of course the real answer is in the code... if (bSep) { snew(buf,256); for(i=0; (iresname[resnr]),resnr+1); cg[ncg].label=strdup(buf); Althogether, this just means that you have multiple charge(d) groups per residue, which are assigned the same label. Let's see, a phosphate a

Re: [gmx-users] Pressure annealing in Gromacs?

On Wed, 2009-12-02 at 10:45 -0500, chris.ne...@utoronto.ca wrote: > Sounds like a phase change. If that is the case, 10 ns is likely not > enough to expect equilibration considering that bilayers can take 50ns > (or even substantially longer) to equilibrate the area per lipid after > a phase

Re: SV: SV: SV: [gmx-users] g_saltbr

Sarah Witzke wrote: In each of the files are a set of distances as a function of time - it does not seem that strange, that the size is equal then. When I plot for instance the four .xvg files mentioned above I get four different curves. Also "diff" lists that every line is different. I

Re: [gmx-users] Exclusions in topology file seem not working for big systems

Thanks for your response Dr van der Spoel. Then there is a limit on the number of atoms that can be defined in the exclusions section. My smaller system has 60 atoms and I used exclusions successfully for that, so I guess the limit might be a little more than 32. Regarding the use of energygr

Re: [gmx-users] For FFamber, should FudgeLJ variable in ffamber.itp be 0.0?

As per my previous post if you read this section more carefully you will see that it mentions the use of RB dihedrals in combination with 1-4 interactions (and tells you not to modify topologies produced by pdb2gmx for these cases!). You only need to exclude 1-4 interactions when using RB's t

Re: [gmx-users] Exclusions in topology file seem not working for big systems

Reza Salari wrote: Hi All, I seem to have a hard time to use exclusions in topology file. I have a relatively big system (~400 aa) that I am trying to calculate the difference in desolvation energy (dA) upon turning off charges on a specific residue using thermodynamics integration method. Th

[gmx-users] Exclusions in topology file seem not working for big systems

Hi All, I seem to have a hard time to use exclusions in topology file. I have a relatively big system (~400 aa) that I am trying to calculate the difference in desolvation energy (dA) upon turning off charges on a specific residue using thermodynamics integration method. The system is a complex

SV: SV: SV: [gmx-users] g_saltbr

Sarah Witzke wrote: >Per the documentation, the only options that can be passed to g_saltbr are > -s >and -f, so no, you cannot use any index groups. > > I thought so :-( > Indeed, Mark's clever suggestion may be useful here. Yes, definitely. > There are no old xvg files in t

[gmx-users] Gromacs 4.0.3 Mopac7 install

Hi everyone: I'm trying of install gromacs with mopac7 support, but it give a classical gromacs-mopac error: ../mdlib/.libs/libmd.so: undefined reference to `__ctype_b' collect2: ld returned 1 exit status make[3]: *** [grompp] Error 1 make[3]: Leaving directory `/usr/local/bio/gromacs-4.0.3/src/k

[gmx-users] Pressure annealing in Gromacs?

Sounds like a phase change. If that is the case, 10 ns is likely not enough to expect equilibration considering that bilayers can take 50ns (or even substantially longer) to equilibrate the area per lipid after a phase change. None of this is to contradict your intuition about a high-temp

Re: [gmx-users] Pressure annealing in Gromacs?

Jussi Lehtola wrote: Hi, I'm experiencing trouble converging the density of some heavy liquid alcohols (after 10 ns of simulation the density is still changing linearly). Is there any way to run pressure annealing in Gromacs? Running the system through a high pressure and temperature might giv

[gmx-users] any chance to write avoid writing out trr but only xtc file ?

Thanks Berk, I agree that a single file open action is not going to cause a lot of system activity. We're simply trying to cut down wherever possible as this is a large shared cluster where the activity of many users distributed amongst 30K cores is overwhelming the GPFS. We have been ins

[gmx-users] Pressure annealing in Gromacs?

Hi, I'm experiencing trouble converging the density of some heavy liquid alcohols (after 10 ns of simulation the density is still changing linearly). Is there any way to run pressure annealing in Gromacs? Running the system through a high pressure and temperature might give an equilibrium struct

RE: [gmx-users] any chance to write avoid writing out trr but only xtc file ?

Hi, We should remove the opening of the trr file in Gromacs 4.1 when no output is requested. But opening one output file on one process should not cause a lot of system activity, independently of the size of the cluster, right? More costly are the fexist operations that all processes perform f

[gmx-users] .cpt file not used for mdrun input in the absence of the -cpi flag

Hello, I have just realized that an existing checkpoint file will not be used as input to mdrun when its name is supplied via -deffnm but not directly via -cpi. I suppose that this makes sense for backward compatibility, and the mdrun -h "-cpi state.cpt Input, Opt. Checkpoint file"

[gmx-users] any chance to write avoid writing out trr but only xtc file ?

We have the same desire on a large cluster in order to reduce the number of file operations overall. In addition to Xavier's suggestion, you can also write your .trr to memory: mdrun -deffnm xx -t /dev/shm/xx.trr or to the local disk: mdrun -deffnm xx -t ${TMPDIR}/xx.trr if those exist and dep

[gmx-users] Re: amber force field in Gromacs

> Dear Servaas, > > In tleap did you really did: > > TLEAP > tleap -f leaprc.ff99SB > ad = sequence { DA5 DA DA3 } > saveamberparm da da_amber.top da_amber.crd > > > If so, it's wrong, it should be: > > saveamberparm ad da_amber.top da_amber.crd > ^^^ > and not 'da' Ye

Re: [gmx-users] Re: any chance to write avoid writing out trr but only xtc file ?

Jörn-Benjamin Lenz wrote: Hi, here is what the is written out if I remove on eof the trr files during the REMD simulation although the xtc files should still be written out. just for your information: I am not out of quota. that I can promise !!! Any ideas why the program behaves like this ?

Re: [gmx-users] Re: any chance to write avoid writing out trr but only xtc file ?

The message is clear, the program does not find the files (trr) anymore. This is expected and trying to understand why it does so seems not really useful. Especially because erasing an output file while the program is running is non-sense, although it might be necessary. Just use the 0 freque

[gmx-users] PMF calculation using g_wham using different simulation boxes

Hi Li, In my opiniun, what you propose is acceptable, but not rigorous, and you will need to prove that there are no unexpected artifacts of changing box size. For example, you should definitely run a couple of your small box systems as larger boxes as well and show that you get the same

[gmx-users] Re: any chance to write avoid writing out trr but only xtc file ?

Hi, here is what the is written out if I remove on eof the trr files during the REMD simulation although the xtc files should still be written out. just for your information: I am not out of quota. that I can promise !!! Any ideas why the program behaves like this ? Is there anything that was ch

Re: [gmx-users] PMF calculation using g_wham using different simulation boxes

Li Jianguo wrote: Hi I am trying to calcualte the potential of mean force between two polyatomic particles using umbrella potential and the g_wham command. I need to run multiple windows from close to far inter-particle distance. To save time, I used smaller box sizes for those windows wit

[gmx-users] Re: amber force field in Gromacs

Dear Servaas, In tleap did you really did: TLEAP tleap -f leaprc.ff99SB ad = sequence { DA5 DA DA3 } saveamberparm da da_amber.top da_amber.crd If so, it's wrong, it should be: saveamberparm ad da_amber.top da_amber.crd ^^^ and not 'da' Besides, I tried to reproduce wh

[gmx-users] PMF calculation using g_wham using different simulation boxes

Hi   I am trying to calcualte the potential of mean force between two polyatomic particles using umbrella potential and the g_wham command. I need to run multiple windows from close to far inter-particle distance. To save time, I used smaller box sizes for those windows with shorter inter-parti

[gmx-users] amber force field in Gromacs

> servaas skrev: > >> Message: 4 > >> Date: Tue, 1 Dec 2009 13:56:21 + > >> From: Alan > >> Subject: [gmx-users] Re: amber force field in Gromacs > >> To: gmx-users@gromacs.org > >> Message-ID: > >> > >> Content-Type: text/plain; charset=UTF-8 > >> > >> Dear Servaas, > >> > >> I've b

Re: [gmx-users] doing averages using g_angle

Amit Choubey wrote: Hi Mark, Ok here is the command line i used :- g_angle -f after_md.trr -type dihedral -n chain1.ndx -b 800 -e 804 -all output is # This file was created Tue Dec 1 20:20:41 2009 # by the following command: # g_angle -f after_md.trr -type dihedral -n chain1.ndx -b 800 -e