Re: [gmx-users] New ion parameters and OPLS-AA
On 12/15/09 11:03 PM, Reza Salari wrote: Thanks for your response. While I will try that (although it seems it needs quite amount of scripting), I remember in the past some people in the mailing list mentioned problems while using nonbond_params directvie with OPLS-AA and in response it was generally suggested to avoid doing this kind of mixing. Like Dr Abraham suggestion here: http://www.mail-archive.com/gmx-users@gromacs.org/msg23147.html Have you tried this kind of mixing for OPLS successfully, without being overridden by the default rules? The main thing that I am still unsure about is how the previously mentioned paper converted the sigma values for different combination rules. It seems that there must be a relatively direct way to do this without going through the re-parametrization process. Unfortunately the combination rules are part of the parameterization, simply because changing the combination rules means changing the parameters. Hence I would suggest you look for ion parameters that are compatible with your force field of choice, alternatively a force field that is compatible with your ions of choice. Since these ion parameters were developed by Tom Cheatham I presume that Amber would be a suitable force field. Regards, Reza Salari *From:* Andrew Paluch apal...@nd.edu *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Tue, December 15, 2009 4:34:18 PM *Subject:* Re: [gmx-users] New ion parameters and OPLS-AA Read the manual. You can explicitly declare all of your cross terms rather than using the same mixing rule for all terms. You can easily write a script to modify your input files accordingly, Andrew On Tue, Dec 15, 2009 at 4:06 PM, Reza Salari resa...@yahoo.com mailto:resa...@yahoo.com wrote: Hi All, Recently there has been a new set of ion parameters published by Joung and Chetham and I am interested in running some test runs using these parameters. These set of parameters are based on using LB rule (arithmetic mean) for sigmas. However I am using OPLS-AA ff so I am using the combination rule 3 (geometric mean of corresponding A and B values). My question is that can I use the exact sigma values from Cheatham for my simulations? I'm almost positive that I have to change these sigma values to be consistent with the combination rule that I am using. In fact there is a paper by Horinek et al that has a nice table of different ionic sigma and epsilon values from different parameter sets (Aqvist, Jensen, Cheatham,..). The article is here: http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normalid=JCPSA60001301212450701idtype=cvipsgifs=Yes http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normalid=JCPSA60001301212450701idtype=cvipsgifs=Yes In that table, they have mentioned two sigmas; a usual sigma (which is used with rule 2) and a sigma prime (which can be used with rule 3). However it seems sort of unclear to me how they got these value since in some references that they've mentioned I could find either sigma or sigma prime, not both. So I am guessing there must be some way to convert these two sigmas to each other. So does anyone know if there is such way? Does GROMACS internally treats sigmas as sigma prime for OPLS-AA? I looked at the manual and also searched the mailing list to find an explanation but without luck. I really appreciate any help on clarifying this. Regards, Reza Salari -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se -- 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 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/mailing_lists/users.php
[gmx-users] freeze group
I running the simulation of a protein with Fe4s4 cluster. The parameters for the cluster were obtained from a previously published paper. I have been able to carry out energy minimization with the following keywords- ; cpp = /usr/bin/cpp define = -DFLEX_SPC constraints = none integrator = steep nsteps = 2000 ; ; Energy minimizing stuff ; emtol = 2000 emstep = 0.01 nstcomm = 1 ns_type = grid rlist = 1 coulombtype = PME rcoulomb = 1.0 rvdw = 1.0 Tcoupl = no Pcoupl = no gen_vel = no -- The output showsSteepest Descents converged to Fmax 2000 in 203 steps Potential Energy = -5.8639745e+06 Maximum force = 1.7305787e+03 on atom 777 Norm of force = 4.4084099e+01 But when I am trying the position retraining step, with following keywords in pr.mdp file- title = Yo cpp = /usr/bin/cpp define = -DPOSRES constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 1 ; total 20.0 ps. nstcomm = 1 nstxout = 250 nstvout = 1000 nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb = 1.0 rvdw = 1.4 ; Berendsen temperature coupling is on Tcoupl = v-rescale tc-grps = Protein SOL SF4 tau_t = 0.1 0.1 0.1 ref_t = 300 300 300 ; Energy monitoring energygrps = Protein SOL SF4 ; Pressure coupling is on Pcoupl = parrinello-rahman tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = 173529 an error is generated with LINCS warningStep 155, time 0.31 (ps) LINCS WARNING relative constraint deviation after LINCS: rms inf, max 14002532367890120704.00 (between atoms 5093 and 5096) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 1193 1195 40.1 0.1330 0.1913 0.1330 1193 1194 38.7 0.1230 0.1757 0.1230 1191 1192 77.7 0.1530 210.9258 0.1530 1189 1193 63.7 0.1530 193.1889 0.1530 1189 1190 75.9 0.1530 193.1568 0.1530 1188 1192 65.6 0.1470 893.4214 0.1470 1188 1189 67.7 0.1470 909.7200 0.1470 1186 1188 72.8 0.1330 3701.8413 0.1330 1186 1187 78.6 0.1230 3824.8157 0.1230 1184 1185 79.5 0.1780 57.6559 0.1780 1183 1184 79.3 0.1829 539.6799 0.1830 1182 1183 85.5 0.1530 3695.6021 0.1530 1181 1186 84.6 0.1530 14910.0859 0.1530 1181 1182 86.6 0.1530 15403.3672 0.1530 1179 1181 87.4 0.1470 35502.0234 0.1470 1179 1180 89.9 0.1000 1119163.2500 0.1000 1177 1179 86.7 0.1330 37732.0156 0.1330 1177 1178 85.9 0.1230 17608.4004 0.1230 1175 1177 99.6 0.1530 50041.0938 0.1530 1175 1176 102.3 0.1530 37907.5586 0.1530 1173 1175 117.7 0.1470 698413.0625 0.1470 1173 1174 120.6 0.1000 677364.4375 0.1000 1171 1173 107.2 0.1330 4168765.5000 0.1330 1171 1172 108.5 0.1230 4103918.2500 0.1230 1169 1170 112.9 0.1090 9872814. 0.1090 1167 1169 92.1 0.1390 68041384. 0.1390t = 0.310 ps: Water molecule starting at atom 196197 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates - These atoms 5093 and 5096 are the Iron atoms of the cluster. Now My question is- a) Can I freeze the movement of the Fe4S4 cluster during simulation by incorporating the cluster in freeze group? b) If yes, then how do I incorporate the freeze group in Pr.mdp file during position restraining step? c) Is there any other alternative to correct the linc warning error? The INTERNET now has a personality. YOURS! See your Yahoo! Homepage. http://in.yahoo.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/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/mailing_lists/users.php
[gmx-users] Denaturation of Proteins by MARTINI Coarse-Graining Forse Field
Dear GMX users, Hi I'm working on denaturation of proteins with MARTINI CGFF by Gromacs suit. according to this paper (J. Chem. Theory and Comput. 2008, 4, 819–834) I undestand there is a limitation for modeling of folding and unfolding with MARITI CGFF for systems in which the folding and unfolding of secondary structures are playing a substantial role are therefore not suitable for modeling with current CG force field. since I perform CGMD simulation on tertiary structure, is there this limitation on my system or no? If your question is positive, Is there an improved version of MARTINI CGFF for doing it? Can I use Gō model for resolve of this problem? What is your idea about this problem? I'm looking forward to hearing from you about this matter! Beast Regards 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/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/mailing_lists/users.php
Re: [gmx-users] Denaturation of Proteins by MARTINI Coarse-Graining Forse Field
Is this a real gromacs-user question? Have your tried to contact the MArtini developers? As a matter of fact some of them have prepared a new MARTINI web-site where a discussion forum will be on. To answer your question: using MARTINI for the unfolding mechanism of proteins would be very challenging to put it nice. It is not AT ALL made for that! The use of Go-model has be tested (for other purposes) and it would be at least as bad as using an all atom FF. No need to use a CG model with Go-models, atomistic are fast enough. Well that is my current opinion. On Dec 16, 2009, at 11:36 AM, rasoul nasiri wrote: Dear GMX users, Hi I'm working on denaturation of proteins with MARTINI CGFF by Gromacs suit. according to this paper (J. Chem. Theory and Comput. 2008, 4, 819– 834) I undestand there is a limitation for modeling of folding and unfolding with MARITI CGFF for systems in which the folding and unfolding of secondary structures are playing a substantial role are therefore not suitable for modeling with current CG force field. since I perform CGMD simulation on tertiary structure, is there this limitation on my system or no? If your question is positive, Is there an improved version of MARTINI CGFF for doing it? Can I use Gō model for resolve of this problem? What is your idea about this problem? I'm looking forward to hearing from you about this matter! Beast Regards 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/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/mailing_lists/users.php -- 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 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/mailing_lists/users.php
Re: [gmx-users] freeze group
subarna thakur wrote: I running the simulation of a protein with Fe4s4 cluster. The parameters for the cluster were obtained from a previously published paper. I have been able to carry out energy minimization with the following keywords- snip *a) Can I freeze the movement of the Fe4S4 cluster during simulation by incorporating the cluster in freeze group?* Can I? and should I? are separate concepts. Of course you can, but would that be useful? See below. *b) If yes, then how do I incorporate the freeze group in Pr.mdp file during position restraining step?* Please read the manual. *c) Is there any other alternative to correct the linc warning error?* I would suggest several things before trying to freeze the cluster artificially. First, choose a more stringent energy minimization criterion. Fmax 2000 is typically insufficient for almost any system. Also, having the cluster as its own separate temperature coupling group is inappropriate. See here, specifically the second point under What Not To Do: http://www.gromacs.org/Documentation/Terminology/Thermostats -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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/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/mailing_lists/users.php
[gmx-users] Frequency confout is updated
Hello, I would like to setup a screensaver to visualize structures as we are simulating them. We want to avoid slowing down the simulation significantly. I found a solution that read pdb files. Is there a way to reduce the frequency mdrun updates the confout.gro? The structure file (-c) contains the coordinates and velocities of the last step -c confout.gro Output Structure file: gro g96 pdb if I increase these values, does it write to these files less frequently or are we stuck with the updating this structure every step? nstxout: (100) [steps] frequency to write coordinates to output trajectory file, the last coordinates are always written nstvout: (100) [steps] frequency to write velocities to output trajectory, the last velocities are always written -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- 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 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/mailing_lists/users.php
Re: [gmx-users] Frequency confout is updated
Jack Shultz wrote: Hello, I would like to setup a screensaver to visualize structures as we are simulating them. We want to avoid slowing down the simulation significantly. I found a solution that read pdb files. Is there a way to reduce the frequency mdrun updates the confout.gro? The structure file (-c) contains the coordinates and velocities of the last step -c confout.gro Output Structure file: gro g96 pdb if I increase these values, does it write to these files less frequently or are we stuck with the updating this structure every step? nstxout: (100) [steps] frequency to write coordinates to output trajectory file, the last coordinates are always written nstvout: (100) [steps] frequency to write velocities to output trajectory, the last velocities are always written The confout.gro file is the last output of mdrun; it is written once (hence coordinates and velocities of the last step) and thus is unaffected by nst* options, which only affect the trajectory. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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/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/mailing_lists/users.php
Re: [gmx-users] Frequency confout is updated
Jack Shultz wrote: Hello, I would like to setup a screensaver to visualize structures as we are simulating them. We want to avoid slowing down the simulation significantly. Not slowing things down significantly is only going to be possible when GROMACS can use a processor that isn't going to get interrupted. I'd recommend refreshing such a screensaver only every 30 seconds or so unless you're intending to run only on one core of multi-core machines. Obviously, test your mileage. The user isn't going to see much action on a desktop machine, anyway. I found a solution that read pdb files. Is there a way to reduce the frequency mdrun updates the confout.gro? The structure file (-c) contains the coordinates and velocities of the last step -c confout.gro Output Structure file: gro g96 pdb if I increase these values, does it write to these files less frequently or are we stuck with the updating this structure every step? nstxout: (100) [steps] frequency to write coordinates to output trajectory file, the last coordinates are always written nstvout: (100) [steps] frequency to write velocities to output trajectory, the last velocities are always written As Justin pointed out, these .mdp options refer to the -t trajectory output, and the -c structure file only receives the final configuration. There's something to be said for you copying the -c mechanism and applying it every few thousand simulation steps to your own intermediate output structure file. The screensaver can simply poll that file. 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/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/mailing_lists/users.php
Re: [gmx-users] New ion parameters and OPLS-AA
Thank you very much Dr Paluch and Dr van der Spoel for your responses. Then it seems it would be safer to use mixing the combination rules as a last resort, although it is comforting to know that other people have used it before successfully. I think I will look for the parameters that are compatible with the OPLS-AA combination rule. Although based on Horinek paper I was sort of hoping that I could convert the parameters for different combination rules. Regards, Reza Salari From: David van der Spoel sp...@xray.bmc.uu.se To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wed, December 16, 2009 3:10:13 AM Subject: Re: [gmx-users] New ion parameters and OPLS-AA On 12/15/09 11:03 PM, Reza Salari wrote: Thanks for your response. While I will try that (although it seems it needs quite amount of scripting), I remember in the past some people in the mailing list mentioned problems while using nonbond_params directvie with OPLS-AA and in response it was generally suggested to avoid doing this kind of mixing. Like Dr Abraham suggestion here: http://www.mail-archive.com/gmx-users@gromacs.org/msg23147.html Have you tried this kind of mixing for OPLS successfully, without being overridden by the default rules? The main thing that I am still unsure about is how the previously mentioned paper converted the sigma values for different combination rules. It seems that there must be a relatively direct way to do this without going through the re-parametrization process. Unfortunately the combination rules are part of the parameterization, simply because changing the combination rules means changing the parameters. Hence I would suggest you look for ion parameters that are compatible with your force field of choice, alternatively a force field that is compatible with your ions of choice. Since these ion parameters were developed by Tom Cheatham I presume that Amber would be a suitable force field. Regards, Reza Salari *From:* Andrew Paluch apal...@nd.edu *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Tue, December 15, 2009 4:34:18 PM *Subject:* Re: [gmx-users] New ion parameters and OPLS-AA Read the manual. You can explicitly declare all of your cross terms rather than using the same mixing rule for all terms. You can easily write a script to modify your input files accordingly, Andrew On Tue, Dec 15, 2009 at 4:06 PM, Reza Salari resa...@yahoo.com mailto:resa...@yahoo.com wrote: Hi All, Recently there has been a new set of ion parameters published by Joung and Chetham and I am interested in running some test runs using these parameters. These set of parameters are based on using LB rule (arithmetic mean) for sigmas. However I am using OPLS-AA ff so I am using the combination rule 3 (geometric mean of corresponding A and B values). My question is that can I use the exact sigma values from Cheatham for my simulations? I'm almost positive that I have to change these sigma values to be consistent with the combination rule that I am using. In fact there is a paper by Horinek et al that has a nice table of different ionic sigma and epsilon values from different parameter sets (Aqvist, Jensen, Cheatham,..). The article is here: http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normalid=JCPSA60001301212450701idtype=cvipsgifs=Yes http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normalid=JCPSA60001301212450701idtype=cvipsgifs=Yes In that table, they have mentioned two sigmas; a usual sigma (which is used with rule 2) and a sigma prime (which can be used with rule 3). However it seems sort of unclear to me how they got these value since in some references that they've mentioned I could find either sigma or sigma prime, not both. So I am guessing there must be some way to convert these two sigmas to each other. So does anyone know if there is such way? Does GROMACS internally treats sigmas as sigma prime for OPLS-AA? I looked at the manual and also searched the mailing list to find an explanation but without luck. I really appreciate any help on clarifying this. Regards, Reza Salari -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala
Re: [gmx-users] New ion parameters and OPLS-AA
Thank you very much. That sounds interesting! BTW, I finally found out that the only way to use parameters developed using different combination rules together, is to define them manually in nonbonding_params section of topology. This sounds a little bit dangerous since it is sort of mixing different approaches. Regards, Reza Salari From: Alexandre Suman de Araujo asara...@if.sc.usp.br To: gmx-users@gromacs.org Sent: Wed, December 16, 2009 11:36:50 AM Subject: Re: [gmx-users] New ion parameters and OPLS-AA If you decide to change the ions parameters, you can use the method described here: http://pubs.acs.org/doi/abs/10.1021/jp064835t?prevSearch=%255Bauthor%253A%2Bde%2BAraujo%255DsearchHistoryKey= It is relatively fast and provide nice parameters. Cheers --Alexandre Suman de Araujo Instituto de Física de São Carlos Universidade de São Paulo São Carlos - Brasil Citando Reza Salari resa...@yahoo.com: Thanks for your response. While I will try that (although it seems it needs quite amount of scripting), I remember in the past some people in the mailing list mentioned problems while using nonbond_params directvie with OPLS-AA and in response it was generally suggested to avoid doing this kind of mixing. Like Dr Abraham suggestion here: http://www.mail-archive.com/gmx-users@gromacs.org/msg23147.html Have you tried this kind of mixing for OPLS successfully, without being overridden by the default rules? The main thing that I am still unsure about is how the previously mentioned paper converted the sigma values for different combination rules. It seems that there must be a relatively direct way to do this without going through the re-parametrization process. Regards, Reza Salari From: Andrew Paluch apal...@nd.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Tue, December 15, 2009 4:34:18 PM Subject: Re: [gmx-users] New ion parameters and OPLS-AA Read the manual. You can explicitly declare all of your cross terms rather than using the same mixing rule for all terms. You can easily write a script to modify your input files accordingly, Andrew On Tue, Dec 15, 2009 at 4:06 PM, Reza Salari resa...@yahoo.com wrote: Hi All, Recently there has been a new set of ion parameters published by Joung and Chetham and I am interested in running some test runs using these parameters. These set of parameters are based on using LB rule (arithmetic mean) for sigmas. However I am using OPLS-AA ff so I am using the combination rule 3 (geometric mean of corresponding A and B values). My question is that can I use the exact sigma values from Cheatham for my simulations? I'm almost positive that I have to change these sigma values to be consistent with the combination rule that I am using. In fact there is a paper by Horinek et al that has a nice table of different ionic sigma and epsilon values from different parameter sets (Aqvist, Jensen, Cheatham,..). The article is here: http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normalid=JCPSA60001301212450701idtype=cvipsgifs=Yes In that table, they have mentioned two sigmas; a usual sigma (which is used with rule 2) and a sigma prime (which can be used with rule 3). However it seems sort of unclear to me how they got these value since in some references that they've mentioned I could find either sigma or sigma prime, not both. So I am guessing there must be some way to convert these two sigmas to each other. So does anyone know if there is such way? Does GROMACS internally treats sigmas as sigma prime for OPLS-AA? I looked at the manual and also searched the mailing list to find an explanation but without luck. I really appreciate any help on clarifying this. Regards, Reza Salari -- 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 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/mailing_lists/users.php Novo Webmail IFSC -- 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 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/mailing_lists/users.php -- 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 don't post (un)subscribe requests to the list. Use the www interface or send it to
Re: [gmx-users] New ion parameters and OPLS-AA
Thank you very much. That sounds interesting! BTW, I finally found out that the only way to use parameters developed using different combination rules together, is to define them manually in nonbonding_params section of topology. This sounds a little bit dangerous since it is sort of mixing different approaches. NO don't do that! You will not be using the same parameters, if you change the combination rules. Regards, Reza Salari *From:* Alexandre Suman de Araujo asara...@if.sc.usp.br *To:* gmx-users@gromacs.org *Sent:* Wed, December 16, 2009 11:36:50 AM *Subject:* Re: [gmx-users] New ion parameters and OPLS-AA If you decide to change the ions parameters, you can use the method described here: http://pubs.acs.org/doi/abs/10.1021/jp064835t?prevSearch=%255Bauthor%253A%2Bde%2BAraujo%255DsearchHistoryKey http://pubs.acs.org/doi/abs/10.1021/jp064835t?prevSearch=%255Bauthor%253A%2Bde%2BAraujo%255DsearchHistoryKey= It is relatively fast and provide nice parameters. Cheers --Alexandre Suman de Araujo Instituto de Física de São Carlos Universidade de São Paulo São Carlos - Brasil Citando Reza Salari resa...@yahoo.com mailto:resa...@yahoo.com: Thanks for your response. While I will try that (although it seems it needs quite amount of scripting), I remember in the past some people in the mailing list mentioned problems while using nonbond_params directvie with OPLS-AA and in response it was generally suggested to avoid doing this kind of mixing. Like Dr Abraham suggestion here: http://www.mail-archive.com/gmx-users@gromacs.org/msg23147.html Have you tried this kind of mixing for OPLS successfully, without being overridden by the default rules? The main thing that I am still unsure about is how the previously mentioned paper converted the sigma values for different combination rules. It seems that there must be a relatively direct way to do this without going through the re-parametrization process. Regards, Reza Salari From: Andrew Paluch apal...@nd.edu mailto:apal...@nd.edu To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org Sent: Tue, December 15, 2009 4:34:18 PM Subject: Re: [gmx-users] New ion parameters and OPLS-AA Read the manual. You can explicitly declare all of your cross terms rather than using the same mixing rule for all terms. You can easily write a script to modify your input files accordingly, Andrew On Tue, Dec 15, 2009 at 4:06 PM, Reza Salari resa...@yahoo.com mailto:resa...@yahoo.com wrote: Hi All, Recently there has been a new set of ion parameters published by Joung and Chetham and I am interested in running some test runs using these parameters. These set of parameters are based on using LB rule (arithmetic mean) for sigmas. However I am using OPLS-AA ff so I am using the combination rule 3 (geometric mean of corresponding A and B values). My question is that can I use the exact sigma values from Cheatham for my simulations? I'm almost positive that I have to change these sigma values to be consistent with the combination rule that I am using. In fact there is a paper by Horinek et al that has a nice table of different ionic sigma and epsilon values from different parameter sets (Aqvist, Jensen, Cheatham,..). The article is here: http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normalid=JCPSA60001301212450701idtype=cvipsgifs=Yes http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normalid=JCPSA60001301212450701idtype=cvipsgifs=Yes In that table, they have mentioned two sigmas; a usual sigma (which is used with rule 2) and a sigma prime (which can be used with rule 3). However it seems sort of unclear to me how they got these value since in some references that they've mentioned I could find either sigma or sigma prime, not both. So I am guessing there must be some way to convert these two sigmas to each other. So does anyone know if there is such way? Does GROMACS internally treats sigmas as sigma prime for OPLS-AA? I looked at the manual and also searched the mailing list to find an explanation but without luck. I really appreciate any help on clarifying this. Regards, Reza Salari -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php Novo Webmail IFSC -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org
Re: [gmx-users] Check for bad contacts and/or reduce the timestep
Hi, I tried energy minimization and I am getting the error while I am running the minimization step. But then I still tried to carry on with normal md-simulation, and it was fine, but I am sure it won't give me the result that it should. Is there a reason for that? I have tried very low energy steps as well, but I am still getting the error. -Nisha Quoting Thomas Schlesier schl...@uni-mainz.de: You can try a normal md-simulation after the energy minimisation, with a very low timestep (around two orders of magnitude lower, for 5ps). For this use no T-couple, or if with, then with a very low temperature. I had a case where i had a box of well ordered benzene molecules and only energyminimization didn't helpt much (In normal md simulation i got many lincs warning form the beginning). After the short NVE-md-simulation the benzene molecules weren't ordered and after a second energy minimization it was possible to do a normal md simulation at 300 K without any lincs warnings. Could be possible that the same protocol works also in your case, else follow Justin's advice. Greetings Thomas Message: 3 Date: Mon, 14 Dec 2009 14:09:47 -0500 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] Check for bad contacts and/or reduce the timestep To: Gromacs Users' List gmx-users@gromacs.org Message-ID: 4b268d7b.1060...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed nishap.pa...@utoronto.ca wrote: snip Steepest Descents converged to machine precision in 34 steps, but did not reach the requested Fmax 10. Potential Energy = -3.7206969e+04 Maximum force = 2.0111207e+04 on atom 1217 Norm of force = 6.9283209e+02 I don't understand constraints I need to turn off, since I haven't mentioned any in my grompp file. This is just generic advice that mdrun provides. The fact is your starting structure contains atomic overlap or clashes that cannot be resolved by energy minimization. Have a look at the trajectory and see if you can get some insight into where things are going wrong (since problematic atom numbers are being printed, and perhaps re-consider how you built your system. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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/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/mailing_lists/users.php -- 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 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/mailing_lists/users.php
Re: [gmx-users] Check for bad contacts and/or reduce the timestep
nishap.pa...@utoronto.ca wrote: Hi, I tried energy minimization and I am getting the error while I am running the minimization step. But then I still tried to carry on with normal md-simulation, and it was fine, but I am sure it won't give me the result that it should. Is there a reason for that? I have tried very low energy steps as well, but I am still getting the error. If minimization still reports the same problems, then what I said before is still true - you have bad contacts somewhere. Have you looked at the trajectory to see where these problematic atoms are and what might be causing the clashes? Sometimes running sufficiently gentle equilibration can relax away some of these bad contacts, but that is rarely the case and often problems will manifest later on in the course of MD. I would seriously consider re-evaluating however you built your system (which you haven't told us) and try to get the energy minimization to actually work before just plowing ahead with fingers crossed. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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/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/mailing_lists/users.php
Re: [gmx-users] New ion parameters and OPLS-AA
Thanks for your response. So basically since the Cheatham parameters are using LB rule, I can never use them with OPLS-AA? I was thinking if I find the parameters for OPLS atoms that are based on geometric rule (if there such a thing exists at all), I could use them along with Cheatham parameters and then define the hetero-atomic LJ parameters in nonbonding_params section. This way I would be mixing parameters that have been developed the same way (regarding combination rules). I understand that one shouldn't directly mix the sigma's that have been developed using different combination rules. If I there is no OPLS parameters based on LB rule, as you mentioned I have to switch to some ff like Amber. Regards, Reza Salari From: David van der Spoel sp...@xray.bmc.uu.se To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wed, December 16, 2009 1:08:58 PM Subject: Re: [gmx-users] New ion parameters and OPLS-AA Thank you very much. That sounds interesting! BTW, I finally found out that the only way to use parameters developed using different combination rules together, is to define them manually in nonbonding_params section of topology. This sounds a little bit dangerous since it is sort of mixing different approaches. NO don't do that! You will not be using the same parameters, if you change the combination rules. Regards, Reza Salari *From:* Alexandre Suman de Araujo asara...@if.sc.usp.br *To:* gmx-users@gromacs.org *Sent:* Wed, December 16, 2009 11:36:50 AM *Subject:* Re: [gmx-users] New ion parameters and OPLS-AA If you decide to change the ions parameters, you can use the method described here: http://pubs.acs.org/doi/abs/10.1021/jp064835t?prevSearch=%255Bauthor%253A%2Bde%2BAraujo%255DsearchHistoryKey http://pubs.acs.org/doi/abs/10.1021/jp064835t?prevSearch=%255Bauthor%253A%2Bde%2BAraujo%255DsearchHistoryKey= It is relatively fast and provide nice parameters. Cheers --Alexandre Suman de Araujo Instituto de Física de São Carlos Universidade de São Paulo São Carlos - Brasil Citando Reza Salari resa...@yahoo.com mailto:resa...@yahoo.com: Thanks for your response. While I will try that (although it seems it needs quite amount of scripting), I remember in the past some people in the mailing list mentioned problems while using nonbond_params directvie with OPLS-AA and in response it was generally suggested to avoid doing this kind of mixing. Like Dr Abraham suggestion here: http://www.mail-archive.com/gmx-users@gromacs.org/msg23147.html Have you tried this kind of mixing for OPLS successfully, without being overridden by the default rules? The main thing that I am still unsure about is how the previously mentioned paper converted the sigma values for different combination rules. It seems that there must be a relatively direct way to do this without going through the re-parametrization process. Regards, Reza Salari From: Andrew Paluch apal...@nd.edu mailto:apal...@nd.edu To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org Sent: Tue, December 15, 2009 4:34:18 PM Subject: Re: [gmx-users] New ion parameters and OPLS-AA Read the manual. You can explicitly declare all of your cross terms rather than using the same mixing rule for all terms. You can easily write a script to modify your input files accordingly, Andrew On Tue, Dec 15, 2009 at 4:06 PM, Reza Salari resa...@yahoo.com mailto:resa...@yahoo.com wrote: Hi All, Recently there has been a new set of ion parameters published by Joung and Chetham and I am interested in running some test runs using these parameters. These set of parameters are based on using LB rule (arithmetic mean) for sigmas. However I am using OPLS-AA ff so I am using the combination rule 3 (geometric mean of corresponding A and B values). My question is that can I use the exact sigma values from Cheatham for my simulations? I'm almost positive that I have to change these sigma values to be consistent with the combination rule that I am using. In fact there is a paper by Horinek et al that has a nice table of different ionic sigma and epsilon values from different parameter sets (Aqvist, Jensen, Cheatham,..). The article is here: http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normalid=JCPSA60001301212450701idtype=cvipsgifs=Yes http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normalid=JCPSA60001301212450701idtype=cvipsgifs=Yes In that table, they have mentioned two sigmas; a usual sigma (which is used with rule 2) and a sigma prime (which can be used with rule 3). However it seems sort of unclear to me how they got these value since in some references
Re: [gmx-users] Check for bad contacts and/or reduce the timestep
Hi Justin, I am trying to plot rdf of one methane molecule in water (spc water, 1095(water molecule in my file). I did create the file using genbox (31.010 31.010 31.010). This is the energy minimization file I am using: title = Methane in water cpp = /lib/cpp include = -I../top integrator = steep emtol = 1.0 nsteps = 100 nstenergy = 10 nstxtcout = 10 xtc_grps= CH4 SOL energygrps = CH4 SOL nstlist = 5 ns_type = simple rlist = 1.0 coulombtype = cut-off rcoulomb= 1.0 rvdw= 1.0 constraints = none pbc = no I tried reducing the steps (to 9 instead of 100) and it works but it doesn't make sense. I am going to try to build the system again. Thanks alot of for help. -Nisha Quoting Justin A. Lemkul jalem...@vt.edu: nishap.pa...@utoronto.ca wrote: Hi, I tried energy minimization and I am getting the error while I am running the minimization step. But then I still tried to carry on with normal md-simulation, and it was fine, but I am sure it won't give me the result that it should. Is there a reason for that? I have tried very low energy steps as well, but I am still getting the error. If minimization still reports the same problems, then what I said before is still true - you have bad contacts somewhere. Have you looked at the trajectory to see where these problematic atoms are and what might be causing the clashes? Sometimes running sufficiently gentle equilibration can relax away some of these bad contacts, but that is rarely the case and often problems will manifest later on in the course of MD. I would seriously consider re-evaluating however you built your system (which you haven't told us) and try to get the energy minimization to actually work before just plowing ahead with fingers crossed. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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/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/mailing_lists/users.php -- 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 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/mailing_lists/users.php
Re: [gmx-users] Check for bad contacts and/or reduce the timestep
nishap.pa...@utoronto.ca wrote: Hi Justin, I am trying to plot rdf of one methane molecule in water (spc water, 1095(water molecule in my file). I did create the file using genbox (31.010 31.010 31.010). This is the energy minimization file I am using: Surely a 31-nm cubic box is excessive for a system of 1095 water molecules. You are aware that Gromacs specifies all units in nm, not Angstrom, right? As for the parameters in the .mdp file, I don't see anything that would necessarily cause the instability you're seeing. A better coulombtype method (in general) is PME, but this may not have a significant effect during the EM procedure. title= Methane in water cpp= /lib/cpp include= -I../top integrator= steep emtol= 1.0 nsteps= 100 nstenergy= 10 nstxtcout= 10 xtc_grps= CH4 SOL energygrps= CH4 SOL nstlist= 5 ns_type= simple rlist= 1.0 coulombtype= cut-off rcoulomb= 1.0 rvdw= 1.0 constraints= none pbc= no I tried reducing the steps (to 9 instead of 100) and it works but it doesn't make sense. I am going to try to build the system again. Reducing the number of steps will actually make the energy minimization worse! If anything, use *more* steps to try to make the structure better. -Justin Thanks alot of for help. -Nisha Quoting Justin A. Lemkul jalem...@vt.edu: nishap.pa...@utoronto.ca wrote: Hi, I tried energy minimization and I am getting the error while I am running the minimization step. But then I still tried to carry on with normal md-simulation, and it was fine, but I am sure it won't give me the result that it should. Is there a reason for that? I have tried very low energy steps as well, but I am still getting the error. If minimization still reports the same problems, then what I said before is still true - you have bad contacts somewhere. Have you looked at the trajectory to see where these problematic atoms are and what might be causing the clashes? Sometimes running sufficiently gentle equilibration can relax away some of these bad contacts, but that is rarely the case and often problems will manifest later on in the course of MD. I would seriously consider re-evaluating however you built your system (which you haven't told us) and try to get the energy minimization to actually work before just plowing ahead with fingers crossed. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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/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/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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/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/mailing_lists/users.php
Re: [gmx-users] Check for bad contacts and/or reduce the timestep
Hi, You are right, I had to delete some water molecules, it is working fine now. Thanks. -Nisha P Quoting Justin A. Lemkul jalem...@vt.edu: nishap.pa...@utoronto.ca wrote: Hi Justin, I am trying to plot rdf of one methane molecule in water (spc water, 1095(water molecule in my file). I did create the file using genbox (31.010 31.010 31.010). This is the energy minimization file I am using: Surely a 31-nm cubic box is excessive for a system of 1095 water molecules. You are aware that Gromacs specifies all units in nm, not Angstrom, right? As for the parameters in the .mdp file, I don't see anything that would necessarily cause the instability you're seeing. A better coulombtype method (in general) is PME, but this may not have a significant effect during the EM procedure. title= Methane in water cpp= /lib/cpp include= -I../top integrator= steep emtol= 1.0 nsteps= 100 nstenergy= 10 nstxtcout= 10 xtc_grps= CH4 SOL energygrps= CH4 SOL nstlist= 5 ns_type= simple rlist= 1.0 coulombtype= cut-off rcoulomb= 1.0 rvdw= 1.0 constraints= none pbc= no I tried reducing the steps (to 9 instead of 100) and it works but it doesn't make sense. I am going to try to build the system again. Reducing the number of steps will actually make the energy minimization worse! If anything, use *more* steps to try to make the structure better. -Justin Thanks alot of for help. -Nisha Quoting Justin A. Lemkul jalem...@vt.edu: nishap.pa...@utoronto.ca wrote: Hi, I tried energy minimization and I am getting the error while I am running the minimization step. But then I still tried to carry on with normal md-simulation, and it was fine, but I am sure it won't give me the result that it should. Is there a reason for that? I have tried very low energy steps as well, but I am still getting the error. If minimization still reports the same problems, then what I said before is still true - you have bad contacts somewhere. Have you looked at the trajectory to see where these problematic atoms are and what might be causing the clashes? Sometimes running sufficiently gentle equilibration can relax away some of these bad contacts, but that is rarely the case and often problems will manifest later on in the course of MD. I would seriously consider re-evaluating however you built your system (which you haven't told us) and try to get the energy minimization to actually work before just plowing ahead with fingers crossed. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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/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/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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/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/mailing_lists/users.php -- 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 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/mailing_lists/users.php
[gmx-users] RDF methanol and water
HI, Okay, so I am trying to plot rdf of one methanol this time in water. Is there a way to select methanol molecule as a whole (i.e. get rdf from the center of the molecule), instead of Me, O and H. Even though I put Me, O and H in same group, I am getting a weird rdf plot (Attached to this message). -Thanks Nisha P # Grace project file # @version 50122 @page size 792, 612 @page scroll 5% @page inout 5% @link page off @map font 8 to Courier, Courier @map font 10 to Courier-Bold, Courier-Bold @map font 11 to Courier-BoldOblique, Courier-BoldOblique @map font 9 to Courier-Oblique, Courier-Oblique @map font 4 to Helvetica, Helvetica @map font 6 to Helvetica-Bold, Helvetica-Bold @map font 7 to Helvetica-BoldOblique, Helvetica-BoldOblique @map font 15 to Helvetica-Narrow, Helvetica-Narrow @map font 16 to Helvetica-Narrow-Bold, Helvetica-Narrow-Bold @map font 17 to Helvetica-Narrow-BoldOblique, Helvetica-Narrow-BoldOblique @map font 18 to Helvetica-Narrow-Oblique, Helvetica-Narrow-Oblique @map font 5 to Helvetica-Oblique, Helvetica-Oblique @map font 20 to NewCenturySchlbk-Bold, NewCenturySchlbk-Bold @map font 21 to NewCenturySchlbk-BoldItalic, NewCenturySchlbk-BoldItalic @map font 22 to NewCenturySchlbk-Italic, NewCenturySchlbk-Italic @map font 23 to NewCenturySchlbk-Roman, NewCenturySchlbk-Roman @map font 24 to Palatino-Bold, Palatino-Bold @map font 25 to Palatino-BoldItalic, Palatino-BoldItalic @map font 26 to Palatino-Italic, Palatino-Italic @map font 27 to Palatino-Roman, Palatino-Roman @map font 12 to Symbol, Symbol @map font 2 to Times-Bold, Times-Bold @map font 3 to Times-BoldItalic, Times-BoldItalic @map font 1 to Times-Italic, Times-Italic @map font 0 to Times-Roman, Times-Roman @map font 33 to ZapfChancery-MediumItalic, ZapfChancery-MediumItalic @map font 13 to ZapfDingbats, ZapfDingbats @map color 0 to (255, 255, 255), white @map color 1 to (0, 0, 0), black @map color 2 to (255, 0, 0), red @map color 3 to (0, 255, 0), green @map color 4 to (0, 0, 255), blue @map color 5 to (255, 255, 0), yellow @map color 6 to (188, 143, 143), brown @map color 7 to (220, 220, 220), grey @map color 8 to (148, 0, 211), violet @map color 9 to (0, 255, 255), cyan @map color 10 to (255, 0, 255), magenta @map color 11 to (255, 165, 0), orange @map color 12 to (114, 33, 188), indigo @map color 13 to (103, 7, 72), maroon @map color 14 to (64, 224, 208), turquoise @map color 15 to (0, 139, 0), green4 @reference date 0 @date wrap off @date wrap year 1950 @default linewidth 1.0 @default linestyle 1 @default color 1 @default pattern 1 @default font 0 @default char size 1.00 @default symbol size 1.00 @default sformat %.8g @background color 0 @page background fill on @timestamp off @timestamp 0.03, 0.03 @timestamp color 1 @timestamp rot 0 @timestamp font 0 @timestamp char size 1.00 @timestamp def Wed Dec 16 15:44:45 2009 @r0 off @link r0 to g0 @r0 type above @r0 linestyle 1 @r0 linewidth 1.0 @r0 color 1 @r0 line 0, 0, 0, 0 @r1 off @link r1 to g0 @r1 type above @r1 linestyle 1 @r1 linewidth 1.0 @r1 color 1 @r1 line 0, 0, 0, 0 @r2 off @link r2 to g0 @r2 type above @r2 linestyle 1 @r2 linewidth 1.0 @r2 color 1 @r2 line 0, 0, 0, 0 @r3 off @link r3 to g0 @r3 type above @r3 linestyle 1 @r3 linewidth 1.0 @r3 color 1 @r3 line 0, 0, 0, 0 @r4 off @link r4 to g0 @r4 type above @r4 linestyle 1 @r4 linewidth 1.0 @r4 color 1 @r4 line 0, 0, 0, 0 @g0 on @g0 hidden false @g0 type XY @g0 stacked false @g0 bar hgap 0.00 @g0 fixedpoint off @g0 fixedpoint type 0 @g0 fixedpoint xy 0.00, 0.00 @g0 fixedpoint format general general @g0 fixedpoint prec 6, 6 @with g0 @world 0, 0, 2, 2 @stack world 0, 0, 0, 0 @znorm 1 @view 0.15, 0.15, 1.15, 0.85 @title Radial distribution @title font 0 @title size 1.50 @title color 1 @subtitle MeO - SOL @subtitle font 0 @subtitle size 1.00 @subtitle color 1 @xaxes scale Normal @yaxes scale Normal @xaxes invert off @yaxes invert off @xaxis on @xaxis type zero false @xaxis offset 0.00 , 0.00 @xaxis bar on @xaxis bar color 1 @xaxis bar linestyle 1 @xaxis bar linewidth 1.0 @xaxis label r @xaxis label layout para @xaxis label place auto @xaxis label char size 1.00 @xaxis label font 0 @xaxis label color 1 @xaxis label place normal @xaxis tick on @xaxis tick major 0.5 @xaxis tick minor ticks 1 @xaxis tick default 6 @xaxis tick place rounded true @xaxis tick in @xaxis tick major size 1.00 @xaxis tick major color 1 @xaxis tick major linewidth 1.0 @xaxis tick major linestyle 1 @xaxis tick major grid off @xaxis tick minor color 1 @xaxis tick minor linewidth 1.0 @xaxis tick minor linestyle 1 @xaxis tick minor grid off @xaxis tick minor size 0.50 @xaxis ticklabel on @xaxis ticklabel format general @xaxis ticklabel prec 5 @xaxis
Re: [gmx-users] RDF methanol and water
nishap.pa...@utoronto.ca wrote: HI, Okay, so I am trying to plot rdf of one methanol this time in water. Is there a way to select methanol molecule as a whole (i.e. get rdf from the center of the molecule), instead of Me, O and H. Even though I put Me, O and H in same group, I am getting a weird rdf plot (Attached to this message). Please read about the options for the -rdf flag of g_rdf. -Justin -Thanks Nisha P -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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/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/mailing_lists/users.php
[gmx-users] Check for bad contacts and/or reduce the timestep
I believe that Justin was suggesting that you move in the opposite direction than to delete some waters. The number density for water should be about 32.5 waters per cubic nanometer, meaning that you should have nearly 1E6 water molecules in a cubic box with sides of 31 nm, and 1095 water molecules should have a box of 33.7 nm^3 (cubic box with sides of 3.23 nm). I suppose that the actual values that you should expect will be slightly lower densities because you are not using pbc. And if Justin was right that you are reporting angstroms in place of nm, then this makes some sense. Still, I can't see how genbox could lead to a box with a density that is too high -- usually it is somewhat too low. I suggest that you diagnose the source of your problem since while simply removing some randomly selected waters appears to have worked for you this time, that would not be a preferable solution to apply to a system any more complex than a single methane in a box of water. Chris. -- original message -- Hi, You are right, I had to delete some water molecules, it is working fine now. Thanks. -Nisha P Quoting Justin A. Lemkul jalemkul at vt.edu: nishap.patel at utoronto.ca wrote: Hi Justin, I am trying to plot rdf of one methane molecule in water (spc water, 1095(water molecule in my file). I did create the file using genbox (31.010 31.010 31.010). This is the energy minimization file I am using: Surely a 31-nm cubic box is excessive for a system of 1095 water molecules. You are aware that Gromacs specifies all units in nm, not Angstrom, right? As for the parameters in the .mdp file, I don't see anything that would necessarily cause the instability you're seeing. A better coulombtype method (in general) is PME, but this may not have a significant effect during the EM procedure. title= Methane in water cpp= /lib/cpp include= -I../top integrator= steep emtol= 1.0 nsteps= 100 nstenergy= 10 nstxtcout= 10 xtc_grps= CH4 SOL energygrps= CH4 SOL nstlist= 5 ns_type= simple rlist= 1.0 coulombtype= cut-off rcoulomb= 1.0 rvdw= 1.0 constraints= none pbc= no I tried reducing the steps (to 9 instead of 100) and it works but it doesn't make sense. I am going to try to build the system again. Reducing the number of steps will actually make the energy minimization worse! If anything, use *more* steps to try to make the structure better. -Justin Thanks alot of for help. -Nisha Quoting Justin A. Lemkul jalemkul at vt.edu: nishap.patel at utoronto.ca wrote: Hi, I tried energy minimization and I am getting the error while I am running the minimization step. But then I still tried to carry on with normal md-simulation, and it was fine, but I am sure it won't give me the result that it should. Is there a reason for that? I have tried very low energy steps as well, but I am still getting the error. If minimization still reports the same problems, then what I said before is still true - you have bad contacts somewhere. Have you looked at the trajectory to see where these problematic atoms are and what might be causing the clashes? Sometimes running sufficiently gentle equilibration can relax away some of these bad contacts, but that is rarely the case and often problems will manifest later on in the course of MD. I would seriously consider re-evaluating however you built your system (which you haven't told us) and try to get the energy minimization to actually work before just plowing ahead with fingers crossed. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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 at gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-request at gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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 at gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-request at gromacs.org. Can't post?
Re: [gmx-users] Frequency confout is updated
Jack Shultz wrote: I guess I misinterpreted the description. I take it there is no built in mechanism to periodically write the structure. There is :-) Trajectory output and checkpoint output. Maybe I could revise the source code to write the structure at every checkpoint? Sure. That's what I was suggesting with my final comment. Find the output mechanism that is used by -c and adapt it for use at the checkpoints. Mark On Wed, Dec 16, 2009 at 10:07 AM, Mark Abraham mark.abra...@anu.edu.au wrote: Jack Shultz wrote: Hello, I would like to setup a screensaver to visualize structures as we are simulating them. We want to avoid slowing down the simulation significantly. Not slowing things down significantly is only going to be possible when GROMACS can use a processor that isn't going to get interrupted. I'd recommend refreshing such a screensaver only every 30 seconds or so unless you're intending to run only on one core of multi-core machines. Obviously, test your mileage. The user isn't going to see much action on a desktop machine, anyway. I found a solution that read pdb files. Is there a way to reduce the frequency mdrun updates the confout.gro? The structure file (-c) contains the coordinates and velocities of the last step -c confout.gro Output Structure file: gro g96 pdb if I increase these values, does it write to these files less frequently or are we stuck with the updating this structure every step? nstxout: (100) [steps] frequency to write coordinates to output trajectory file, the last coordinates are always written nstvout: (100) [steps] frequency to write velocities to output trajectory, the last velocities are always written As Justin pointed out, these .mdp options refer to the -t trajectory output, and the -c structure file only receives the final configuration. There's something to be said for you copying the -c mechanism and applying it every few thousand simulation steps to your own intermediate output structure file. The screensaver can simply poll that file. 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/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/mailing_lists/users.php -- 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 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/mailing_lists/users.php
[gmx-users] Frequency confout is updated
You could also have a script that you optimize for your specific system that knows the number of frames in the xtc based on the file size and then trjconv -dump when your .xtc-polling script sees that it has been updated? Your visualization program could then update based on the output pdb. I realize that this may create unnecessarily large .xtc files -- yet another reason to desire the ability for mdrun to concurrently write a secondary .xtc file that contains only a .ndx-defined subset of the system (in addition to the regular full atom .xtc). Still, you could cycle your mdrun and periodically purge the unnecessarily verbose .xtc that you use mostly for visualization. Chris. Jack Shultz wrote: I guess I misinterpreted the description. I take it there is no built in mechanism to periodically write the structure. There is :-) Trajectory output and checkpoint output. Maybe I could revise the source code to write the structure at every checkpoint? Sure. That's what I was suggesting with my final comment. Find the output mechanism that is used by -c and adapt it for use at the checkpoints. Mark On Wed, Dec 16, 2009 at 10:07 AM, Mark Abraham Mark.Abraham at anu.edu.au wrote: Jack Shultz wrote: Hello, I would like to setup a screensaver to visualize structures as we are simulating them. We want to avoid slowing down the simulation significantly. Not slowing things down significantly is only going to be possible when GROMACS can use a processor that isn't going to get interrupted. I'd recommend refreshing such a screensaver only every 30 seconds or so unless you're intending to run only on one core of multi-core machines. Obviously, test your mileage. The user isn't going to see much action on a desktop machine, anyway. I found a solution that read pdb files. Is there a way to reduce the frequency mdrun updates the confout.gro? The structure file (-c) contains the coordinates and velocities of the last step -c confout.gro Output Structure file: gro g96 pdb if I increase these values, does it write to these files less frequently or are we stuck with the updating this structure every step? nstxout: (100) [steps] frequency to write coordinates to output trajectory file, the last coordinates are always written nstvout: (100) [steps] frequency to write velocities to output trajectory, the last velocities are always written As Justin pointed out, these .mdp options refer to the -t trajectory output, and the -c structure file only receives the final configuration. There's something to be said for you copying the -c mechanism and applying it every few thousand simulation steps to your own intermediate output structure file. The screensaver can simply poll that file. Mark -- gmx-users mailing listgmx-users at gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-request at gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- 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 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/mailing_lists/users.php
[gmx-users] sulfate atomtype for ffgmx
Dear all, I would like to perform MD simulations on a molecule that contains a carbon chain with a sulfonyl (R-SO2-R) group in between. When looking at the available atomtypes for ffgmx I didnt find a sulfate S. Only sulfur (S) and DMSO sulphur atomtypes are available. In literature I did find GROMACS simulations performed on systems with a sulfate group but all of them used the standard Sulfur atomtype. So my question; Would it be reasonable to use the sulfur atomtype for a sulfonyl group R-SO2-R? (as done previously in literature) If not, is there a sulfate atomtype available for ffgmx or would you recommend me to use another force field such as CHARMM for this system? Kind regards, Michiel - SECURITY/CONFIDENTIALITY WARNING: This message and any attachments are intended solely for the individual or entity to which they are addressed. This communication may contain information that is privileged, confidential, or exempt from disclosure under applicable law (e.g., personal health information, research data, financial information). Because this e-mail has been sent without encryption, individuals other than the intended recipient may be able to view the information, forward it to others or tamper with the information without the knowledge or consent of the sender. If you are not the intended recipient, or the employee or person responsible for delivering the message to the intended recipient, any dissemination, distribution or copying of the communication is strictly prohibited. If you received the communication in error, please notify the sender immediately by replying to this message and deleting the message and any accompanying files from your system. If, due to the security risks, you do not wish to receive further communications via e-mail, please reply to this message and inform the sender that you do not wish to receive further e-mail from the sender. - -- 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 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/mailing_lists/users.php
Re: [gmx-users] sulfate atomtype for ffgmx
Niesen, Michiel wrote: Dear all, I would like to perform MD simulations on a molecule that contains a carbon chain with a sulfonyl (R-SO2-R) group in between. When looking at the available atomtypes for ffgmx I didnt find a sulfate S. Only sulfur (S) and DMSO sulphur atomtypes are available. In literature I did find GROMACS simulations performed on systems with a sulfate group but all of them used the standard Sulfur atomtype. If there is precedent, you may be able to use it. However, you should be warned that ffgmx is considered a deprecated force field, and in the absence of a very compelling reason to use it, probably isn't a wise choice. There are many (newer) versions of Gromos force fields that are probably more reliable. So my question; Would it be reasonable to use the sulfur atomtype for a sulfonyl group R-SO2-R? (as done previously in literature) If not, is there a sulfate atomtype available for ffgmx or would you recommend me to use another force field such as CHARMM for this system? There are numerous sulfur atom types in OPLS-AA that may be usable. Have a look at the .atp file to see. CHARMM is not yet officially supported in Gromacs, so that force field probably isn't a viable option. -Justin Kind regards, Michiel - SECURITY/CONFIDENTIALITY WARNING: This message and any attachments are intended solely for the individual or entity to which they are addressed. This communication may contain information that is privileged, confidential, or exempt from disclosure under applicable law (e.g., personal health information, research data, financial information). Because this e-mail has been sent without encryption, individuals other than the intended recipient may be able to view the information, forward it to others or tamper with the information without the knowledge or consent of the sender. If you are not the intended recipient, or the employee or person responsible for delivering the message to the intended recipient, any dissemination, distribution or copying of the communication is strictly prohibited. If you received the communication in error, please notify the sender immediately by replying to this message and deleting the message and any accompanying files from your system. If, due to the security risks, you do not wish to receive further communications via e-mail, please reply to this message and inform the sender that you do not wish to receive further e-mail from the sender. - -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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/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/mailing_lists/users.php
Re: [gmx-users] typo in ffoplsaanb.itp for opls_179 (OS) and opls_180 (OS)
Thanks for the info. pb. On Mon, Dec 14, 2009 at 11:33 PM, Mark Abraham mark.abra...@anu.edu.auwrote: Pradip Biswas wrote: Hi, The atomic numbers of the atom types opls_179 (OS) and opls_180 (OS) are typed in as 7 in ffoplsaanb.itp instead of 8. Accordingly, while doing QMMM, these oxygen atoms are being recognized as Nitrogen atoms. DvdS fixed this in the git source earlier this week. 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/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/mailing_lists/users.php -- Pradip K Biswas, PhD Acting Chair, Department of Physics, Computational Bioscience and Bioengineering Group Tougaloo College, MS 39174 Ph: 601-977-7788 Fax: 601-977-7898 -- 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 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/mailing_lists/users.php
Re: [gmx-users] Problem with Gromacs-CPMD
Hi Jorge, I'll appreciate if you can send me (biswas...@gmail.com) the following files if the problem still persists: 1. output.mdrun_em 2. qm_cpmd.log Also please let me know which version of CPMD you are using. best, pb. On Thu, Nov 19, 2009 at 1:59 PM, jorge_quint...@ciencias.uis.edu.co wrote: Dear all, I'm running some simulations using Gromacs/CPMD but it doesn't continue during QMCONTINUE file lecture. See below: EXTERNAL ENERGY= 5.867019924829098E-002 AU REAL TOTAL ENERGY = -97.3517503273190 AU ATOM COORDINATESGRADIENTS (-FORCES) 1 C 7.2410 9.0551 9.8394 7.709E-02 -3.867E-02 -2.540E-02 12 Cu 7.2410 14.2141 6.4946 -5.854E-04 -6.465E-03 1.232E-02 INTERFACE| FORCES WRITTEN TO FILE RESTART INFORMATION WRITTEN ON FILE ./RESTART.1 === INTERFACE| WAIT FOR CONTINUE-FILE ./QMCONTINUE === Here! At this point my simulations don't continue. A appreciate your support!! Jorge R. Quintero Universidad Industrial de Santander Bucaramanga, Santander - Colombia -- 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 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/mailing_lists/users.php -- Pradip K Biswas, PhD Acting Chair, Department of Physics, Computational Bioscience and Bioengineering Group Tougaloo College, MS 39174 Ph: 601-977-7788 Fax: 601-977-7898 -- 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 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/mailing_lists/users.php
