Re: [gmx-users] Re: comparison of gromacs in CENTOS and UBUNTU
Alexandre Suman de Araujo wrote: Obviously the HD space has nothing to do with GMX performance (unless it is full, of course), but the use of Ubuntu precompiled packages can affect drastically the GMX performance, especially if you are also using pre-compiled MPI library package. An important rule when you are interested in High Performance Computing: Compile ALL your softwares (the last REALLY stable version) using GOOD compilers (GCC is fine, but if you have access to Intel or Portland ones is better). This rule is highly recommended ALSO to your linux kernel. Never leave the important and easy work of compile your important programs with unknown people! Caveat that you need to be reasonably competent at compiling software at least for your machine and those pieces of software in order to be assured you're not doing a worse job then those maligned nameless people. Acquiring the necessary expertise is something of a hit-and-miss process, and so I would leave things like MPI and FFTW libraries and kernels alone to the supervision of people who think they know about them. Perhaps one could try some different versions of libraries to find the best one, or make some inquiries about the experience of the person who compiled the library to help judge. Then also, consult the available documentation for the things you do compile and experiment suitably. For GROMACS, a straight configure make install is rather unlikely to be suitable, these days. 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] problem with topolbuild execution
Hello I am trying to generate a .itp file of a Fe4S4 cluster from mol2 file with the help of topolbuild1_2_1 programm but a error is comming during execution stating Illegal characters for size information line. I dont know what is wrong with the input file. I am giving here the input mol2 file I am using- -- @TRIPOSMOLECULE SF4_ideal.pdb 8 12 0 0 0 SMALL GASTEIGER Energy = 0 @TRIPOSATOM 1 FE1 -0.1560 1.1840 1.4740 Fe 1 SF41 0.2771 2 FE2 1.4550 -1.1820 0.2890 Fe 1 SF41 0.2779 3 FE3 0.3020 0.9990 -1.5840 Fe 1 SF41 0.2526 4 FE4 -1.6010 -1.0010 -0.1800 Fe 1 SF41 0.2284 5 S1 0.1560 -1.1840 -1.4740 S.3 1 SF41 0.2379 6 S2 -1.4550 1.1820 -0.2890 S.3 1 SF41 0.2356 7 S3 -0.3020 -0.9990 1.5840 S.3 1 SF41 0.2487 8 S4 1.6010 1.0010 0.1800 S.3 1 SF41 0.2414 @TRIPOSBOND 1 1 6 1 2 1 7 1 3 1 8 1 4 2 5 1 5 2 7 1 6 2 8 1 7 3 5 1 8 3 6 1 9 3 8 1 10 4 5 1 11 4 6 1 12 4 7 1 @TRIPOS --- Please suggest the changes I should make in the input file to execute the topolbuild programm Regards Subarna Thkaur Looking for local information? Find it on Yahoo! Local http://in.local.yahoo.com/ sf4.mol2 Description: Binary data ___ 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] Re: genconf
Payman, Such little charge cannot produce large energies, so it seems you should run EM first and everything will be OK with your simulation. As far as understand non-zero charge is a resuts of averaging errors (during grompp!), you cannot remove this warning. ~ Vitaly On Wed, Jul 22, 2009 at 3:04 AM, Payman Pirzadeh ppirz...@ucalgary.cawrote: OK! Thanks for the tips on thermostat. I multiplied my .gro file by using the command “genconf”. My original box has non-zero charge, but the generated bigger box has some charges: NOTE 2 [file sixsitemodel.top, line 8]: System has non-zero total charge: -1.220703e-04 Then, during minimization, the system experiences a large positive potential and infinite force. Is there a technicality in using “genconf” that I am missing? Doesn’t it read the dimensions of the box from .gro file to make sure no particles are overlapping with the original box? Or no particle is coming from the new one in the old one? Payman *From:* gmx-users-boun...@gromacs.org [mailto: gmx-users-boun...@gromacs.org] *On Behalf Of *Vitaly V. Chaban *Sent:* July 21, 2009 4:53 PM *To:* gmx-users@gromacs.org *Subject:* [gmx-users] Re: reliability of NOTES Hello, I am trying to prepare the input files for an MD run. After running grompp, I received the following note: NOTE 1 [file npt.mdp, line unknown]: The Berendsen thermostat does not generate the correct kinetic energy distribution. You might want to consider using the V-rescale thermostat. How reliable this note is? It's true. And how can I implement V-rescale thermostat in y input file (I found nothing in the manual). Substitute berendsen with V-rescale in the mdp file. Also, when I changed the thermostat to nose-hoover, it said that it can not be used with Berendsen barostat. Why? C'est la vie... -- Vitaly V. Chaban, Ph.D. (ABD) School of Chemistry V.N. Karazin Kharkiv National University Svoboda sq.,4, Kharkiv 61077, Ukraine email: cha...@univer.kharkov.ua,vvcha...@gmail.com skype: vvchaban, mob.: +38-097-8259698 http://www-rmn.univer.kharkov.ua/chaban.html === !!! Looking for a postdoctoral position !!! === ___ 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] Re: genconf
Vitaly V. Chaban wrote: Payman, Such little charge cannot produce large energies, so it seems you should run EM first and everything will be OK with your simulation. As far as understand non-zero charge is a resuts of averaging errors (during grompp!), you cannot remove this warning. That's not quite right. It results from the fact that binary floating point operations accrue error both from inexact representation of many exact decimal values (e.g. 0.02 has no exact representation, and so added to itself N times, need not equal N*0.02) and from limited precision (to 3 digits, 123 + 0.123 = 123). The former is occurring with the sum of atomic charges in grompp. The latter can occur during the integration, for example. 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] first and second neighbours
Hi, Where May I find a Non-bonded interactions to be excluded (first and second neighbours). – Pair interactions (1-4 interactions) in Gromcas ? Thanks Luis Scott -- Prof. Dr. Luis Paulo Scott CMCC- Centro de Matemática, Computação e Cognição Universidade Federal do ABC Grupo de Pesquisa em Biologia Computacional ___ 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] first and second neighbours
Luis Paulo wrote: Hi, Where May I find a Non-bonded interactions to be excluded (first and second neighbours). – Pair interactions (1-4 interactions) in Gromcas ? I don't understand the question. Thanks Luis Scott -- Prof. Dr. Luis Paulo Scott CMCC- Centro de Matemática, Computação e Cognição Universidade Federal do ABC Grupo de Pesquisa em Biologia Computacional ___ 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 -- 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
RE: [gmx-users] genconf
Thanks a lot Mark! I will run the system for equilibration and then try to replicate it. I will keep you guys posted. Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Mark Abraham Sent: July 21, 2009 11:01 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] genconf Payman Pirzadeh wrote: Yes and no! Sometimes there is an overlap, but sometimes I could find nothing! In the simplest case, how can we avoid overlaps in a way that the crystal structure is maintained under pbc? Can the option -dist help here? Replicating a box that was not designed for periodicity will always have this problem. Whether the box is too small or two large, there will either be steric clashes, or vacuums that will need filling. The general solution is to equilibrate your box under PBC prior to replication. Now the box size and the atomic spacings will be plausible, and the replication will not of necessity introduce artifacts. 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] Periodic Boundary Condition Issues
Hello, I am trying to analyze the trajectory of the estrogen receptor alpha in water. As you know, the ER is a dimer and as such when it approaches the boundary for the simulation one of the monomers jumps to the other side of my box and thus screws up any post simulation calculations that we are interested in, especially since the focus of our project is the dimerization interface. Is there any way to fix this so that visually the dimer doesn't appear to split? Thanks, David ___ 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] trr and xtc
Dear all, I did a simulation of spce water and every thing seemed ok, when I did mdrun -s file.tpr -o file.trr -c file_out.gro -v -g file.log, I got a file.trr with zero size, but I have file.xtc that seems fine with VMD. I don't what happened here. Any idea? Also I looked at the box size from first file.gro and last file_out.gro. It shows the box size has been changed a little bit: first it was 1.86206 1.86206 1.86206 finally it is 1.86586 1.86586 1.86586 Can someone please kindly make it clear to me why it happened? Thanks, Jamie ___ 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] Periodic Boundary Condition Issues
Cooper, David R wrote: Hello, I am trying to analyze the trajectory of the estrogen receptor alpha in water. As you know, the ER is a dimer and as such when it approaches the boundary for the simulation one of the monomers jumps to the other side of my box and thus screws up any post simulation calculations that we are interested in, especially since the focus of our project is the dimerization interface. Is there any way to fix this so that visually the dimer doesn’t appear to split? The trjconv -pbc options were designed to fix this sort of issue. Dimers and complexes can be a bit tricky, so you'll have to play around with different options to find the one that works for you. -Justin Thanks, David ___ 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 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] trr and xtc
Jamie Seyed wrote: Dear all, I did a simulation of spce water and every thing seemed ok, when I did mdrun -s file.tpr -o file.trr -c file_out.gro -v -g file.log, I got a file.trr with zero size, but I have file.xtc that seems fine with VMD. I don't what happened here. Any idea? What did you set as nstxout and nstvout? Depending on what you set for these parameters, you may not get much in the .trr file; the final frame should have been written, however. Maybe something went wrong with the filesystem (a blip), and the output was suppressed. I've had that happen when a simulation is finishing and a .gro file is written, but has nothing in it. Also I looked at the box size from first file.gro and last file_out.gro. It shows the box size has been changed a little bit: first it was 1.86206 1.86206 1.86206 finally it is 1.86586 1.86586 1.86586 What kind of pressure coupling are you using (if any)? Can someone please kindly make it clear to me why it happened? In general, posting the text of your .mdp file is a good idea. That way, the answers to my questions above are answered :) -Justin Thanks, Jamie ___ 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 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] trr and xtc
Hi Justin, nstxout=0 nstvout=0 Pcoupl=berendsen Pcoupltype=isotropic In fact I used the mdp file of /tuto/water and I modified it for PME and v-rescale. But the rest is the same (I am using version 4.0.5) I finished the simulation but I saw file.trr is empty... the rest seems fine...even file.xtc Thank you, Jamie On Wed, Jul 22, 2009 at 11:32 AM, Justin A. Lemkul jalem...@vt.edu wrote: Jamie Seyed wrote: Dear all, I did a simulation of spce water and every thing seemed ok, when I did mdrun -s file.tpr -o file.trr -c file_out.gro -v -g file.log, I got a file.trr with zero size, but I have file.xtc that seems fine with VMD. I don't what happened here. Any idea? What did you set as nstxout and nstvout? Depending on what you set for these parameters, you may not get much in the .trr file; the final frame should have been written, however. Maybe something went wrong with the filesystem (a blip), and the output was suppressed. I've had that happen when a simulation is finishing and a .gro file is written, but has nothing in it. Also I looked at the box size from first file.gro and last file_out.gro. It shows the box size has been changed a little bit: first it was 1.86206 1.86206 1.86206 finally it is 1.86586 1.86586 1.86586 What kind of pressure coupling are you using (if any)? Can someone please kindly make it clear to me why it happened? In general, posting the text of your .mdp file is a good idea. That way, the answers to my questions above are answered :) -Justin Thanks, Jamie ___ 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 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] trr and xtc
Jamie Seyed wrote: Hi Justin, nstxout=0 nstvout=0 Right, then the .trr file should be empty until the very end, when the last frame should be written. Like I said, probably a filesystem blip. Pcoupl=berendsen Pcoupltype=isotropic Note that all of your box vectors are the same at the end. This is probably a consequence of isotropic pressure coupling. -Justin In fact I used the mdp file of /tuto/water and I modified it for PME and v-rescale. But the rest is the same (I am using version 4.0.5) I finished the simulation but I saw file.trr is empty... the rest seems fine...even file.xtc Thank you, Jamie On Wed, Jul 22, 2009 at 11:32 AM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Jamie Seyed wrote: Dear all, I did a simulation of spce water and every thing seemed ok, when I did mdrun -s file.tpr -o file.trr -c file_out.gro -v -g file.log, I got a file.trr with zero size, but I have file.xtc that seems fine with VMD. I don't what happened here. Any idea? What did you set as nstxout and nstvout? Depending on what you set for these parameters, you may not get much in the .trr file; the final frame should have been written, however. Maybe something went wrong with the filesystem (a blip), and the output was suppressed. I've had that happen when a simulation is finishing and a .gro file is written, but has nothing in it. Also I looked at the box size from first file.gro and last file_out.gro. It shows the box size has been changed a little bit: first it was 1.86206 1.86206 1.86206 finally it is 1.86586 1.86586 1.86586 What kind of pressure coupling are you using (if any)? Can someone please kindly make it clear to me why it happened? In general, posting the text of your .mdp file is a good idea. That way, the answers to my questions above are answered :) -Justin Thanks, Jamie ___ gmx-users mailing listgmx-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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu/ | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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] trr and xtc
Thank you Justin, But how I can prevent from that (filesystem blip) to happen. Also May I change Pcoupl= Parrinello-rahman instead of berendsen (has it any effect?? since I have changed Tcoupl=v-rescale instead of berendsen)? By the way there was a warning after doing grompp, it said unknown or double left-hand 'bd-temp' in parameter file In file.mdp it is bd-temp=300 What about this warning related to the problem...?? Thanks, Jamie On Wed, Jul 22, 2009 at 11:53 AM, Justin A. Lemkul jalem...@vt.edu wrote: Jamie Seyed wrote: Hi Justin, nstxout=0 nstvout=0 Right, then the .trr file should be empty until the very end, when the last frame should be written. Like I said, probably a filesystem blip. Pcoupl=berendsen Pcoupltype=isotropic Note that all of your box vectors are the same at the end. This is probably a consequence of isotropic pressure coupling. -Justin In fact I used the mdp file of /tuto/water and I modified it for PME and v-rescale. But the rest is the same (I am using version 4.0.5) I finished the simulation but I saw file.trr is empty... the rest seems fine...even file.xtc Thank you, Jamie On Wed, Jul 22, 2009 at 11:32 AM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: Jamie Seyed wrote: Dear all, I did a simulation of spce water and every thing seemed ok, when I did mdrun -s file.tpr -o file.trr -c file_out.gro -v -g file.log, I got a file.trr with zero size, but I have file.xtc that seems fine with VMD. I don't what happened here. Any idea? What did you set as nstxout and nstvout? Depending on what you set for these parameters, you may not get much in the .trr file; the final frame should have been written, however. Maybe something went wrong with the filesystem (a blip), and the output was suppressed. I've had that happen when a simulation is finishing and a .gro file is written, but has nothing in it. Also I looked at the box size from first file.gro and last file_out.gro. It shows the box size has been changed a little bit: first it was 1.86206 1.86206 1.86206 finally it is 1.86586 1.86586 1.86586 What kind of pressure coupling are you using (if any)? Can someone please kindly make it clear to me why it happened? In general, posting the text of your .mdp file is a good idea. That way, the answers to my questions above are answered :) -Justin Thanks, Jamie ___ gmx-users mailing listgmx-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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu/ | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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
[gmx-users] Re: genconf
Payman, What system fo you try to simulate? How was the initial configuration generated? Did you do EM of the small box before using genconf? Anyway, try to decrease the time step (several orders) and start a small (~1000 steps) MD run. If you experience the overlaps of the particles it should help to get a better configuration. - This is to be fast. Vitaly On Wed, Jul 22, 2009 at 5:18 PM, Payman Pirzadeh ppirz...@ucalgary.cawrote: Hi Vitaly, Problem is when I minimized the system, the potential energy will become sth positive of the order of 10^21 and the force experienced by an atom becomes infinity. This will cause the simulation to crash! Payman *From:* Vitaly V. Chaban [mailto:vvcha...@gmail.com] *Sent:* July 22, 2009 2:20 AM *To:* Payman Pirzadeh; gmx-users@gromacs.org *Subject:* Re: genconf Payman, Such little charge cannot produce large energies, so it seems you should run EM first and everything will be OK with your simulation. As far as understand non-zero charge is a resuts of averaging errors (during grompp!), you cannot remove this warning. ~ Vitaly On Wed, Jul 22, 2009 at 3:04 AM, Payman Pirzadeh ppirz...@ucalgary.ca wrote: OK! Thanks for the tips on thermostat. I multiplied my .gro file by using the command “genconf”. My original box has non-zero charge, but the generated bigger box has some charges: NOTE 2 [file sixsitemodel.top, line 8]: System has non-zero total charge: -1.220703e-04 Then, during minimization, the system experiences a large positive potential and infinite force. Is there a technicality in using “genconf” that I am missing? Doesn’t it read the dimensions of the box from .gro file to make sure no particles are overlapping with the original box? Or no particle is coming from the new one in the old one? Payman *From:* gmx-users-boun...@gromacs.org [mailto: gmx-users-boun...@gromacs.org] *On Behalf Of *Vitaly V. Chaban *Sent:* July 21, 2009 4:53 PM *To:* gmx-users@gromacs.org *Subject:* [gmx-users] Re: reliability of NOTES Hello, I am trying to prepare the input files for an MD run. After running grompp, I received the following note: NOTE 1 [file npt.mdp, line unknown]: The Berendsen thermostat does not generate the correct kinetic energy distribution. You might want to consider using the V-rescale thermostat. How reliable this note is? It's true. And how can I implement V-rescale thermostat in y input file (I found nothing in the manual). Substitute berendsen with V-rescale in the mdp file. Also, when I changed the thermostat to nose-hoover, it said that it can not be used with Berendsen barostat. Why? C'est la vie... -- Vitaly V. Chaban, Ph.D. (ABD) School of Chemistry V.N. Karazin Kharkiv National University Svoboda sq.,4, Kharkiv 61077, Ukraine email: cha...@univer.kharkov.ua,vvcha...@gmail.com skype: vvchaban, mob.: +38-097-8259698 http://www-rmn.univer.kharkov.ua/chaban.html === !!! Looking for a postdoctoral position !!! === ___ 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] Peptide - DMPC membrane simulations - Unstable system
Hi Justin, So after struggling through ... I have confirmed that the error was due to Gromacs version incompatibility. Now my simulation is past problematic step and continues running without any error. Also I am following your advice and also doing the same simulation but with two equilibration steps as per your tutorial. The pressure equilibration step had generated 7Gb *.trr file, is this normal for 10ns equilibration? I have used mdp files from tutorial too. I have question about COM (center of mass) parameters. What happens if we forget about them and do not do the grouping of Solvent+Na+ + Cl- and Protein+DMPC, what could happen? The layer will slide past each other, or what? And one more question about your tutuorial and my previous experiences: Also when I was running InflateGRO my box size incread 4x, so it became huge, 25x25x25, and after compression by 0.95 factor is was around 22x22x22. Therefore I have used the box that we had in the lab already. Is this normal, because visiaully lipids are too spaced out and that's why water enters btwn them when you solvate, to the poin that I wrote C++ program that removes water from lipid bilayer. ___ 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] Re: trr and xtc
Jamie, To have a trajectory in TRR you should just change nstxout=0 nstvout=0 to non-zeros. -- Vitaly V. Chaban, Ph.D. (ABD) School of Chemistry V.N. Karazin Kharkiv National University Svoboda sq.,4, Kharkiv 61077, Ukraine email: cha...@univer.kharkov.ua,vvcha...@gmail.com skype: vvchaban, mob.: +38-097-8259698 http://www-rmn.univer.kharkov.ua/chaban.html === !!! Looking for a postdoctoral position !!! === ___ 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] Peptide - DMPC membrane simulations - Unstable system
Kirill Bessonov wrote: Hi Justin, So after struggling through ... I have confirmed that the error was due to Gromacs version incompatibility. Now my simulation is past problematic step and continues running without any error. Also I am following your advice and also doing the same simulation but with two equilibration steps as per your tutorial. The pressure equilibration step had generated 7Gb *.trr file, is this normal for 10ns equilibration? Depending on how many atoms you have in your system and how often you are saving coordinates and velocities, it could be. If you're using my .mdp files from the tutorial, note that you should probably never use nstxout = 100 for a 10 ns equilibration :) I use small values for short equilibrations so I can catch enough frames in case there's a crash. I have used mdp files from tutorial too. I have question about COM (center of mass) parameters. What happens if we forget about them and do not do the grouping of Solvent+Na+ + Cl- and Protein+DMPC, what could happen? The layer will slide past each other, or what? Yes, the water goes one way, the bilayer goes the other way, and overall there is no COM motion. I believe the problems manifest themselves if you are trying to calculate diffusion coefficients and perhaps other parameters. And one more question about your tutuorial and my previous experiences: Also when I was running InflateGRO my box size incread 4x, so it became huge, 25x25x25, and after compression by 0.95 factor is was around 22x22x22. Therefore I have used the box that we had in the lab already. Is this normal, because visiaully lipids are too spaced out and that's why water enters btwn them when you solvate, to the poin that I wrote C++ program that removes water from lipid bilayer. As specified in my tutorial, you have to run InflateGRO *many* times to return the box to normal dimensions. I believe I used 25 or 26 iterations (scaling by 0.95 each time, followed by EM) to return my system to a reasonable area per lipid. -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 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] Missing G53A6 parameters
Hello everyone. I'm trying to do a simulation with the 53A6 parameters of a molecule that contains a sulfur atom bonded to a CH1 atom and a nitrogen atom. There are no bonded parameters (bond, angle, dihedral) for these combinations. Does anyone have any idea what I could do about that? Should I resort to QM calculations? Thank you. ___ 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] trr and xtc
Jamie Seyed wrote: Thank you Justin, But how I can prevent from that (filesystem blip) to happen. Also May I I know nothing about your filesystem, but sometimes these things happen randomly. Try re-running with nstxout at some value other than zero and see if you get a non-empty .trr file. change Pcoupl= Parrinello-rahman instead of berendsen (has it any effect?? since I have changed Tcoupl=v-rescale instead of berendsen)? Haphazardly changing algorithms for T- and P-coupling without knowing why is a recipe for disaster. Read the literature about each methodology, and choose the one that's appropriate. The problem regarding box dimensions you pointed out before is related to the fact that you are using isotropic pressure coupling, wherein the box dimensions scale uniformly. That will be the case regardless of which algorithm you use. If the box dimensions change, that's just reality :) If for some reason you want to fix the box dimensions, use Pcoupl = no. By the way there was a warning after doing grompp, it said unknown or double left-hand 'bd-temp' in parameter file In file.mdp it is bd-temp=300 What about this warning related to the problem...?? The .mdp file was generated using an old version of Gromacs. Refer to the manual for changes, and delete that line from the .mdp file. -Justin Thanks, Jamie On Wed, Jul 22, 2009 at 11:53 AM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Jamie Seyed wrote: Hi Justin, nstxout=0 nstvout=0 Right, then the .trr file should be empty until the very end, when the last frame should be written. Like I said, probably a filesystem blip. Pcoupl=berendsen Pcoupltype=isotropic Note that all of your box vectors are the same at the end. This is probably a consequence of isotropic pressure coupling. -Justin In fact I used the mdp file of /tuto/water and I modified it for PME and v-rescale. But the rest is the same (I am using version 4.0.5) I finished the simulation but I saw file.trr is empty... the rest seems fine...even file.xtc Thank you, Jamie On Wed, Jul 22, 2009 at 11:32 AM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Jamie Seyed wrote: Dear all, I did a simulation of spce water and every thing seemed ok, when I did mdrun -s file.tpr -o file.trr -c file_out.gro -v -g file.log, I got a file.trr with zero size, but I have file.xtc that seems fine with VMD. I don't what happened here. Any idea? What did you set as nstxout and nstvout? Depending on what you set for these parameters, you may not get much in the .trr file; the final frame should have been written, however. Maybe something went wrong with the filesystem (a blip), and the output was suppressed. I've had that happen when a simulation is finishing and a .gro file is written, but has nothing in it. Also I looked at the box size from first file.gro and last file_out.gro. It shows the box size has been changed a little bit: first it was 1.86206 1.86206 1.86206 finally it is 1.86586 1.86586 1.86586 What kind of pressure coupling are you using (if any)? Can someone please kindly make it clear to me why it happened? In general, posting the text of your .mdp file is a good idea. That way, the answers to my questions above are answered :) -Justin Thanks, Jamie ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto: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 mailto:gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate
Re: [gmx-users] Missing G53A6 parameters
Michael McGovern wrote: Hello everyone. I'm trying to do a simulation with the 53A6 parameters of a molecule that contains a sulfur atom bonded to a CH1 atom and a nitrogen atom. There are no bonded parameters (bond, angle, dihedral) for these combinations. Does anyone have any idea what I could do about that? Should I resort to QM calculations? Thank you. Refer to the original reference for the force field derivation. Many bonded parameters come from spectroscopic data, IIRC. -Justin ___ gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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 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] Missing G53A6 parameters
Michael McGovern wrote: Thanks a lot for the response. They are derived from spectroscopic data. You're saying I should find more spectroscopic data? For consistency with the force field, yes. Otherwise you'll have to have some compelling reason for reviewers as to why any QM calculations are necessary. -Justin --- On Wed, 7/22/09, Justin A. Lemkul jalem...@vt.edu wrote: From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] Missing G53A6 parameters To: mpmcgov...@wisc.edu, Discussion list for GROMACS users gmx-users@gromacs.org Date: Wednesday, July 22, 2009, 1:14 PM Michael McGovern wrote: Hello everyone. I'm trying to do a simulation with the 53A6 parameters of a molecule that contains a sulfur atom bonded to a CH1 atom and a nitrogen atom. There are no bonded parameters (bond, angle, dihedral) for these combinations. Does anyone have any idea what I could do about that? Should I resort to QM calculations? Thank you. Refer to the original reference for the force field derivation. Many bonded parameters come from spectroscopic data, IIRC. -Justin ___ gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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 Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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] using two different combination rules for the LJ potential
Hello, I am trying to simulate a system composed of two different molecules. I made the topology files for each of the two molecules and I did some tests to validate the force-field parameters for my system. I do have all the correct parameters for my system but it turns out that for the two types of molecules I must use two different combination rules of the LJ potential (the combination rule 1 and the combination rule 3). I did some tests using Gromacs and it seems that I can specify the directive [ defaults ] only one time. The manual seems to indicate that I might be able to do something about the combination rules by including a [ nonbond_params ] section in an *.itp file. However, I don;t seem to understand the effect of the [ nonbond_params ] directive onto the [ defaults ] directive normally found in the *.itp file. It seems to me that there is no combination rule specified in the under the [ nonbond_params ] section. Could someone please explain to me how this works? In addition/alternatively, does anyone have any suggestions on how I could go about creating a successful set of topology files using two different combination rules for the LJ potential? Thank you very much for your kind consideration, Ana West Emory University, U.S.A ___ 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] How to cap a peptide using pdb2gmx
Hi everybody I downloaded a pdb entry from RCSB and it comes with charged terminii, for example, the first aminoacid is ATOM 1 N ASN A 1 -8.901 4.127 -0.555 1.00 0.00 N ATOM 2 CA ASN A 1 -8.608 3.135 -1.618 1.00 0.00 C ATOM 3 C ASN A 1 -7.117 2.964 -1.897 1.00 0.00 C ATOM 4 O ASN A 1 -6.634 1.849 -1.758 1.00 0.00 O ATOM 5 CB ASN A 1 -9.437 3.396 -2.889 1.00 0.00 C ATOM 6 CG ASN A 1 -10.915 3.130 -2.611 1.00 0.00 C ATOM 7 OD1 ASN A 1 -11.269 2.700 -1.524 1.00 0.00 O ATOM 8 ND2 ASN A 1 -11.806 3.406 -3.543 1.00 0.00 N ATOM 9 H1 ASN A 1 -8.330 3.957 0.261 1.00 0.00 H ATOM 10 H2 ASN A 1 -8.740 5.068 -0.889 1.00 0.00 H ATOM 11 H3 ASN A 1 -9.877 4.041 -0.293 1.00 0.00 H ATOM 12 HA ASN A 1 -8.930 2.162 -1.239 1.00 0.00 H ATOM 13 HB2 ASN A 1 -9.310 4.417 -3.193 1.00 0.00 H ATOM 14 HB3 ASN A 1 -9.108 2.719 -3.679 1.00 0.00 H ATOM 15 HD21 ASN A 1 -11.572 3.791 -4.444 1.00 0.00 H ATOM 16 HD22 ASN A 1 -12.757 3.183 -3.294 1.00 0.00 H and the same goes for the last one I need to use ACE and NME for the terminii, so I tried using the -ter option in the pdb2gmx command, but when I use it it says N-terminus: none C-terminus: none and don't let me choose any terminii. Any ideas. Thanks in advance -- Camilo Andrés Jiménez Cruz ___ 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] How to cap a peptide using pdb2gmx
Camilo Andrés Jimenez Cruz wrote: Hi everybody I downloaded a pdb entry from RCSB and it comes with charged terminii, for example, the first aminoacid is ATOM 1 N ASN A 1 -8.901 4.127 -0.555 1.00 0.00 N ATOM 2 CA ASN A 1 -8.608 3.135 -1.618 1.00 0.00 C ATOM 3 C ASN A 1 -7.117 2.964 -1.897 1.00 0.00 C ATOM 4 O ASN A 1 -6.634 1.849 -1.758 1.00 0.00 O ATOM 5 CB ASN A 1 -9.437 3.396 -2.889 1.00 0.00 C ATOM 6 CG ASN A 1 -10.915 3.130 -2.611 1.00 0.00 C ATOM 7 OD1 ASN A 1 -11.269 2.700 -1.524 1.00 0.00 O ATOM 8 ND2 ASN A 1 -11.806 3.406 -3.543 1.00 0.00 N ATOM 9 H1 ASN A 1 -8.330 3.957 0.261 1.00 0.00 H ATOM 10 H2 ASN A 1 -8.740 5.068 -0.889 1.00 0.00 H ATOM 11 H3 ASN A 1 -9.877 4.041 -0.293 1.00 0.00 H ATOM 12 HA ASN A 1 -8.930 2.162 -1.239 1.00 0.00 H ATOM 13 HB2 ASN A 1 -9.310 4.417 -3.193 1.00 0.00 H ATOM 14 HB3 ASN A 1 -9.108 2.719 -3.679 1.00 0.00 H ATOM 15 HD21 ASN A 1 -11.572 3.791 -4.444 1.00 0.00 H ATOM 16 HD22 ASN A 1 -12.757 3.183 -3.294 1.00 0.00 H and the same goes for the last one I need to use ACE and NME for the terminii, so I tried using the -ter option in the pdb2gmx command, but when I use it it says N-terminus: none C-terminus: none and don't let me choose any terminii. Any ideas. The coordinates for the cap must be present in the .pdb file. -Justin Thanks in advance -- Camilo Andrés Jiménez Cruz ___ 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 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] residue-residue specific energy plots
Is there any utility/tool out there that can take an outputted GROMACS trajectory, and output the energies (electric potential, VDW, etc.) of all residue-residue specific interactions as a function of time? The g_energy utility does not give me the data I want, and it will not even allow you to index and compare two residues. Thanks, Jon ___ 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] residue-residue specific energy plots
Jonathan Reyles wrote: Is there any utility/tool out there that can take an outputted GROMACS trajectory, and output the energies (electric potential, VDW, etc.) of all residue-residue specific interactions as a function of time? The g_energy utility does not give me the data I want, and it will not even allow you to index and compare two residues. You can if you utilize energygrps in the .mdp file, listing all of the residues of interest. This will, naturally, make the .edr file enormous, but you can then extract any or all of these residue-residue pairs using g_energy. -Justin Thanks, Jon ___ 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 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] trr and xtc
Hi, On Wed, Jul 22, 2009 at 1:13 PM, Justin A. Lemkul jalem...@vt.edu wrote: Jamie Seyed wrote: Thank you Justin, But how I can prevent from that (filesystem blip) to happen. Also May I I know nothing about your filesystem, but sometimes these things happen randomly. Try re-running with nstxout at some value other than zero and see if you get a non-empty .trr file. Yes, It is ok now. I re-run it with nonzero nstxout ! Thanks for all comments. change Pcoupl= Parrinello-rahman instead of berendsen (has it any effect?? since I have changed Tcoupl=v-rescale instead of berendsen)? Haphazardly changing algorithms for T- and P-coupling without knowing why is a recipe for disaster. Read the literature about each methodology, and choose the one that's appropriate. The problem regarding box dimensions you pointed out before is related to the fact that you are using isotropic pressure coupling, wherein the box dimensions scale uniformly. That will be the case regardless of which algorithm you use. If the box dimensions change, that's just reality :) If for some reason you want to fix the box dimensions, use Pcoupl = no. By the way there was a warning after doing grompp, it said unknown or double left-hand 'bd-temp' in parameter file In file.mdp it is bd-temp=300 What about this warning related to the problem...?? The .mdp file was generated using an old version of Gromacs. Refer to the manual for changes, and delete that line from the .mdp file. -Justin Thanks, Jamie On Wed, Jul 22, 2009 at 11:53 AM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: Jamie Seyed wrote: Hi Justin, nstxout=0 nstvout=0 Right, then the .trr file should be empty until the very end, when the last frame should be written. Like I said, probably a filesystem blip. Pcoupl=berendsen Pcoupltype=isotropic Note that all of your box vectors are the same at the end. This is probably a consequence of isotropic pressure coupling. -Justin In fact I used the mdp file of /tuto/water and I modified it for PME and v-rescale. But the rest is the same (I am using version 4.0.5) I finished the simulation but I saw file.trr is empty... the rest seems fine...even file.xtc Thank you, Jamie On Wed, Jul 22, 2009 at 11:32 AM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Jamie Seyed wrote: Dear all, I did a simulation of spce water and every thing seemed ok, when I did mdrun -s file.tpr -o file.trr -c file_out.gro -v -g file.log, I got a file.trr with zero size, but I have file.xtc that seems fine with VMD. I don't what happened here. Any idea? What did you set as nstxout and nstvout? Depending on what you set for these parameters, you may not get much in the .trr file; the final frame should have been written, however. Maybe something went wrong with the filesystem (a blip), and the output was suppressed. I've had that happen when a simulation is finishing and a .gro file is written, but has nothing in it. Also I looked at the box size from first file.gro and last file_out.gro. It shows the box size has been changed a little bit: first it was 1.86206 1.86206 1.86206 finally it is 1.86586 1.86586 1.86586 What kind of pressure coupling are you using (if any)? Can someone please kindly make it clear to me why it happened? In general, posting the text of your .mdp file is a good idea. That way, the answers to my questions above are answered :) -Justin Thanks, Jamie ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto: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 mailto:gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php --
RE: [gmx-users] genconf
Hello, I minimized the initial output (from another simulation) first; then I replicated it. This time, the minimization of the bigger box was done more easily! I ran an MD simulation with the bigger box and after 6 hours, it has not crashed yet. But, I have a question. When we replicate a box, and in the primary box one molecule is dissected into pieces due to pbc, will GROMACS return the molecules to its original shape during MD run or not? I believe, without minimization, these dissected pieces will remain in the middle of the box and interfere with their replicated versions. Maybe, 'genconf' should be modified for such replications to maintain the pbc between the new molecules at the boundaries and fix the problem with the particle in the middle of the new bigger box! Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Payman Pirzadeh Sent: July 22, 2009 9:22 AM To: 'Discussion list for GROMACS users' Subject: RE: [gmx-users] genconf Thanks a lot Mark! I will run the system for equilibration and then try to replicate it. I will keep you guys posted. Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Mark Abraham Sent: July 21, 2009 11:01 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] genconf Payman Pirzadeh wrote: Yes and no! Sometimes there is an overlap, but sometimes I could find nothing! In the simplest case, how can we avoid overlaps in a way that the crystal structure is maintained under pbc? Can the option -dist help here? Replicating a box that was not designed for periodicity will always have this problem. Whether the box is too small or two large, there will either be steric clashes, or vacuums that will need filling. The general solution is to equilibrate your box under PBC prior to replication. Now the box size and the atomic spacings will be plausible, and the replication will not of necessity introduce artifacts. 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 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] genconf
Payman Pirzadeh wrote: Hello, I minimized the initial output (from another simulation) first; then I replicated it. This time, the minimization of the bigger box was done more easily! I ran an MD simulation with the bigger box and after 6 hours, it has not crashed yet. But, I have a question. When we replicate a box, and in the primary box one molecule is dissected into pieces due to pbc, will GROMACS return the molecules to its original shape during MD run or not? No, it does not. I believe, without minimization, these dissected pieces will remain in the middle of the box and interfere with their replicated versions. Maybe, 'genconf' should be modified for such replications to maintain the pbc between the new molecules at the boundaries and fix the problem with the particle in the middle of the new bigger box! It can easily be accomplished using a .tpr file, and by using trjconv -pbc whole. After molecules are whole, then use genconf. -Justin Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Payman Pirzadeh Sent: July 22, 2009 9:22 AM To: 'Discussion list for GROMACS users' Subject: RE: [gmx-users] genconf Thanks a lot Mark! I will run the system for equilibration and then try to replicate it. I will keep you guys posted. Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Mark Abraham Sent: July 21, 2009 11:01 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] genconf Payman Pirzadeh wrote: Yes and no! Sometimes there is an overlap, but sometimes I could find nothing! In the simplest case, how can we avoid overlaps in a way that the crystal structure is maintained under pbc? Can the option -dist help here? Replicating a box that was not designed for periodicity will always have this problem. Whether the box is too small or two large, there will either be steric clashes, or vacuums that will need filling. The general solution is to equilibrate your box under PBC prior to replication. Now the box size and the atomic spacings will be plausible, and the replication will not of necessity introduce artifacts. 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 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 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] Zn parameterization
Hello, I am curious - is there anyway to see what assumptions were made when parameterizing the Zn 2+ ion? Was it tetrahedrally or octahedrally coordinated? With waters only or with imidazoles? Do the different force fields make different assumptions? Guidance appreciated. Regards, Marc___ 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] Zn parameterization
Marc Charendoff wrote: Hello, I am curious - is there anyway to see what assumptions were made when parameterizing the Zn 2+ ion? Was it tetrahedrally or octahedrally coordinated? With waters only or with imidazoles? Do the different force fields make different assumptions? Guidance appreciated. Without even knowing the force field to which you were referring, we can't say anything other than to refer you to the primary literature for that force field. 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] using two different combination rules for the LJ potential
Ana West wrote: Hello, I am trying to simulate a system composed of two different molecules. I made the topology files for each of the two molecules and I did some tests to validate the force-field parameters for my system. I do have all the correct parameters for my system but it turns out that for the two types of molecules I must use two different combination rules of the LJ potential (the combination rule 1 and the combination rule 3). That suggests you're mixing force fields, which is a bad idea. In any case, you can convert between these parameter forms easily (see manual section 5.3.3). Obviously, compare outputs between the old combination rule parameters and the converted ones to check your conversion. I did some tests using Gromacs and it seems that I can specify the directive [ defaults ] only one time. The manual seems to indicate that I might be able to do something about the combination rules by including a [ nonbond_params ] section in an *.itp file. However, I don;t seem to understand the effect of the [ nonbond_params ] directive onto the [ defaults ] directive normally found in the *.itp file. It seems to me that there is no combination rule specified in the under the [ nonbond_params ] section. Could someone please explain to me how this works? There is one combination rule available, specified in [ defaults ] and used everywhere required. This is sound methodology. In addition/alternatively, does anyone have any suggestions on how I could go about creating a successful set of topology files using two different combination rules for the LJ potential? Depending on the underlying reason, probably don't do it. For a start, when an atom whose parameters are of combination type 1 interacts with an atom whose parameters are of combination type 3, you would need to pre-compute their interaction and describe that in [ nonbond_params ]. That's rapidly tedious as the number of atoms grows. 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] genconf
Payman Pirzadeh wrote: Thanks a lot Mark! I will run the system for equilibration and then try to replicate it. I will keep you guys posted. Obviously, equilibrating under PBC NPT will allow the box to change size to suit the system... PBC NVT won't, so you can end up with unsuitable density. 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
