[gmx-users] Optimal Hardware for Gromacs
Hi, there is a question for hardware experts. What is the optimal hardware to achieve better scalability in parallel MD simulations of 10K-100K atoms? Probably, it should be a cluster of multi-cpu, multi-core units with fast interconnection. In this case, what is the optimal=performance/price configuration for the units? Or in greater details the choice should be: 1) Intel or AMD? 2) Server cpus (Xeon/Opteron) or Desktop cpus (i7/Phenom)? (The problem is that for the cheaper option (Desktop cpus) there is no multi-cpu motherboards available on a market. May be somebody knows the appropriate MB model.) 3) 4-, 6- or 8-core cpus? See Opteron 6134 which has 8 cores of 2.3 Ghz. 4) Is there network solution faster than 1 Gbps for a reasonable price? Or may be the optimum is some preassembled workstation or cluster available on a market for a reasonable price. Resuming the subject: what is the optimal hardware with a budget ~$10K? April 2010 -- 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] Optimal Hardware for Gromacs
On 4/28/10 9:38 AM, Igor Leontyev wrote: Hi, there is a question for hardware experts. What is the optimal hardware to achieve better scalability in parallel MD simulations of 10K-100K atoms? Probably, it should be a cluster of multi-cpu, multi-core units with fast interconnection. In this case, what is the optimal=performance/price configuration for the units? Or in greater details the choice should be: 1) Intel or AMD? 2) Server cpus (Xeon/Opteron) or Desktop cpus (i7/Phenom)? (The problem is that for the cheaper option (Desktop cpus) there is no multi-cpu motherboards available on a market. May be somebody knows the appropriate MB model.) 3) 4-, 6- or 8-core cpus? See Opteron 6134 which has 8 cores of 2.3 Ghz. 4) Is there network solution faster than 1 Gbps for a reasonable price? Or may be the optimum is some preassembled workstation or cluster available on a market for a reasonable price. Resuming the subject: what is the optimal hardware with a budget ~$10K? April 2010 Try finding a local vendor to sell you Supermicro based machines. $10k should get you roughly 4 dual quad core Intel or AMD with Infiniband network, 32 cores altogether in a rack (with some haggling). The machines with more cores per chip are usually overprized. -- David. David van der Spoel, PhD, Professor of Biology Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 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] simulated annealing (SA)
Hi gromacs users about SA simulation, I saw in some papers that annealing _time is very short. fpr example [The temperature was increased from 0 to 600 K over the first 4 ps, held at 600 K for 2 ps, and then slowly cooled to 0 K over 14 ps in simulation of protein-dna]. Is there limitation in election of annealing _time? what is optimum value for annealing _time? Any help will highly appreciated! -- 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] RDF
Hello, On 27.04.2010, at 23:31, Nilesh Dhumal wrote: Hello, I am trying to plot radial distribution function between a atom and a center of two atoms. How can I calculate the centre of two atoms and further how can I use this center to plot radial distribution funciton? you will have to use an index file including the group containing the atom and a group containing the other two atoms. Then take a look at the help of g_rdf (g_rdf -h). There are several flags which determine the reference points used to calculate the RDF in your case it should be -rdf mol_cog. /Flo THanks Nilesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests 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 -- Florian Dommert Dipl.-Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart Phone: +49(0)711/685-6-3613 Fax: +49-(0)711/685-6-3658 EMail: domm...@icp.uni-stuttgart.de Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert PGP.sig Description: This is a digitally signed message part -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests 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] g_wham giving flat free energy
Michael McGovern wrote: Hi everyone. I'm having some trouble using g_wham to analyze some results. I have some simulations from gromacs 3.3 using the pull code. I'm using the latest version of g_wham to analyze the results, which the help file says is ok, using the -ip option. I've gotten almost everything to work, and it generates histograms that seem perfectly reasonable, but sometimes the free energy it outputs is completely flat, with each bin having a free energy value of 0. I've played around with the -b and -e options using only part of my data, and sometimes it gives non-flat free energies, other times not. I see no logic to when it works and when it doesn't. My data does have good overlap of the histograms, and it sometimes converges even when I use data that have no overlaps, so that doesn't seem to be the problem. I'm completely confused. Does anyone know what could cause this? Hi Micheal, how large is your data? Could you send me a tar.gz of your pdo files? I would like to make sure that there is no bug in g_wham. Jochen -- --- Dr. Jochen Hub Molecular Biophysics group Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4714451 Fax: +46-18-511755 --- -- 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: how many dihedral angles should be included for the naphthalene molecule if I use oplsaa
I second Justin here, for Amber FF (which share essentially the same topology but with different parameters with OPLS/AA), the impropers dihedrals seems to be enough as for TRP. Just a side note, using ACPYPE (which uses antechamber in the core) to generate topologies for molecules like TRP, 6 extra impr. dihedrals are added, but clearly not necessary. You may want to try ACPYPE as I believe antechamber does a really good job getting the topology (even if in excess of imp. dih as for TRP and probably for napthalene), and of course check the literature as suggested by Justin. Alan On Wed, Apr 28, 2010 at 06:13, gmx-users-requ...@gromacs.org wrote: Ming Han wrote: 1__2 6__ // 3\/ \\ |||4| \\___ /\___// 5 7 I want to know if 1-2-3-6 torsion should be included? And if both 2-3-4-7 and 6-3-4-5 should be included? Thanks. I would think that proper dihedrals would not even be used for such a molecule. The fused ring systems will utilize impropers to stay planar. For example, the TRP side chain specifies no proper dihedrals within the indole side chain; only impropers are used, but maybe someone with more OPLS derivation experience can comment. You can also look into the literature. A simple Google search for napthalene OPLS (without the quotes) turns up tons of simulation papers. -Justin -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- 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] Freezing a portion of a protein during simulation
Hello Justin, In my topology file I am declaring: --- ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Strong position restraints on rest of B2AR #ifdef STRONG_POSRES #include strong_posre.itp #endif ; Include water topology #include spc.itp - And in my .mdp file I am giving: - define = -DSTRONG_POSRES ; Run parameters integrator = md; leap-frog integrator nsteps = 5000 ; 2 * 5 = 100 ps dt = 0.002 ; 2 fs --- But now what I am getting is that if I run MD using these restraints on the helical portion of the protein, then I am getting LINCS errors. However, if I allow the entire protein to move during MD, then it is running fine. What mistake am I making? And how can I freeze properly the helical portions and simulate only the loop? Thanks a lot in advance. Regards, Anirban On Fri, Apr 23, 2010 at 5:37 PM, Justin A. Lemkul jalem...@vt.edu wrote: Anirban Ghosh wrote: Hi ALL, I want to do a MD simulation by restraining (freezing) the helical portions and allowing only the loop regions to move. I tried doing this by applying heavy restrain on the helical residues by generating a .itp file with the genrestr command with an index file containing the desired residue numbers. However during the simulation I am finding that the entire protein is moving. Am I doing anything wrong? Or is there any other way to freeze a portion of a protein? Any suggestion is welcome. thanks a lot in advance. If your protein is still moving, then you aren't correctly applying your position restraints. Without seeing your topology and .mdp file, there's no way to know what you're doing wrong. You can also use the freezegrps option in the .mdp file, but then you also have to make sure you're using the appropriate energygrp_excl, etc. It is generally much easier to apply position restraints. -Justin Regards, Anirban -- 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] Freezing a portion of a protein during simulation
Anirban Ghosh wrote: Hello Justin, In my topology file I am declaring: --- ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Strong position restraints on rest of B2AR #ifdef STRONG_POSRES #include strong_posre.itp #endif What is in strong_posre.itp? Presumably you're only restraining certain residues, right? Did you create this with genrestr and an appropriate index group? ; Include water topology #include spc.itp - And in my .mdp file I am giving: - define = -DSTRONG_POSRES ; Run parameters integrator = md; leap-frog integrator nsteps = 5000 ; 2 * 5 = 100 ps dt = 0.002 ; 2 fs --- If this is the entirety of your .mdp file, you're asking for trouble. Allowing all other parameters to be taken as default is very dangerous, and probably inappropriate (most notably cutoff electrostatics). But now what I am getting is that if I run MD using these restraints on the helical portion of the protein, then I am getting LINCS errors. However, if I allow the entire protein to move during MD, then it is running fine. What mistake am I making? And how can I freeze properly the helical portions and simulate only the loop? Thanks a lot in advance. Recognize that there is a difference between freezing and restraining. Read in the manual about what freezing is versus position restraints. Either way, you should be able to get things up and running, but position restraints are a bit easier to implement. If an unrestrained simulation runs fine (using that fragmented .mdp file?) then there are probably just bad clashes in the system that the restraints are not allowing to relax. -Justin Regards, Anirban On Fri, Apr 23, 2010 at 5:37 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Anirban Ghosh wrote: Hi ALL, I want to do a MD simulation by restraining (freezing) the helical portions and allowing only the loop regions to move. I tried doing this by applying heavy restrain on the helical residues by generating a .itp file with the genrestr command with an index file containing the desired residue numbers. However during the simulation I am finding that the entire protein is moving. Am I doing anything wrong? Or is there any other way to freeze a portion of a protein? Any suggestion is welcome. thanks a lot in advance. If your protein is still moving, then you aren't correctly applying your position restraints. Without seeing your topology and .mdp file, there's no way to know what you're doing wrong. You can also use the freezegrps option in the .mdp file, but then you also have to make sure you're using the appropriate energygrp_excl, etc. It is generally much easier to apply position restraints. -Justin Regards, Anirban -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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 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] more than one peptide in one simulation box
shahid nayeem wrote: Hi Justin Should I try to do position restraint at 500k and then full MD simulation. Always equilibrate under the conditions you wish to use prior to collecting data under those conditions. As for whether or not your force field is even valid at such high temperature is another question, but I know there is a substantial body of literature regarding high-temperature MD, so you may want to do some reading to understand the pros and cons of what you're trying to do. -Justin shahid On 4/27/10, *Justin A. Lemkul* jalem...@vt.edu mailto:jalem...@vt.edu wrote: shahid nayeem wrote: My peptide is 26 residue alpha helix obtained from crystal structure .pdb file. I am posting energy minimization, position restarint and full MD simulation .mdp file snip ref_t = 300 300 Here, you're equilibrating at 300 K... snip ref_t = 500 500 and here, you're running MD at 500 K, without any equilibration in between. That could be a problem, but more likely, the high temperature is simply causing the structure to break down. Short helices are usually not stable in isolation, and heating them to extreme conditions will probably accelerate this process. The various results you're seeing with different helices may just reflect that you haven't simulated long enough to see convergence in the structural features, but from what you've described, I expect what you're seeing is entirely normal, and almost predictable. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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 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] simulated annealing (SA)
shahab shariati wrote: Hi gromacs users about SA simulation, I saw in some papers that annealing _time is very short. fpr example [The temperature was increased from 0 to 600 K over the first 4 ps, held at 600 K for 2 ps, and then slowly cooled to 0 K over 14 ps in simulation of protein-dna]. Is there limitation in election of annealing _time? what is optimum value for annealing _time? The time necessary will depend on the size of the system and the degree to which temperature affects it. You may have to play around a bit to determine what is reasonable for your system, and if whatever you're doing accomplishes whatever goal you have for the SA procedure. -Justin Any help will highly appreciated! -- 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] 1-4 interaction and Buckingham potential
Dear All, How is the 1-4 interaction treated when using Buckingham potential for vdw type of interactions in gromacs? As I understand from the manual one has to delete the [ pairs ] section in the topology file (if present) and the the scaling for 1-4 interaction will be 1.0. Did I get it right? Another issue is that whether the 1-4 scaling by 1.0 is correct or not for Buckingham. Anybody with an opinion on this? Terveisin, Markus -- --www=http://www.iki.fi/markus.kaukonen --markus.kauko...@iki.fi --office: N102 Nano building FIN-02015 TKK --home: Viinirinne 3 F 12, 02630 Espoo, FIN --tel: h 045-1242068, w 4518694, 050-5112785 --Rikos ei kannata, eika maatalous --Suomessa. (Paimio 1998) --- -- --www=http://www.iki.fi/markus.kaukonen --markus.kauko...@iki.fi --office: N102 Nano building FIN-02015 TKK --home: Viinirinne 3 F 12, 02630 Espoo, FIN --tel: h 045-1242068, w 4518694, 050-5112785 --Rikos ei kannata, eika maatalous --Suomessa. (Paimio 1998) --- -- 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] implicit solvent simulation in gromacs
Hi All, I want to perform MD simulation of a protein in implicit solvent using gromacs 4.0.7. I looked into the manual but did not get any information regarding the implicit solvent. Is it avilable in gromacs? I searched in the mailing list and found someone in older mail said its not avilable. If it is avilable, could anybody please give me the mdp option. Is it okay to use 43a1 FF? Thanks Chanchal -- 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] 64-bit gromacs-4.0.7 for Mac OSX
Dear all, With gromacs-4.0.5, one had the possibility to compile a 64-bit version of gromacs for Mac OS X using configure -- enable-apple-64bit. This was even suggested by configure to improve performance. With gromacs-4.0.7, the option --enable-apple-64bit of configure has disappeared and configure no longer suggests to compile in 64-bit. Is this no longer recommended for Mac OSX? Thanks for your time, Rui Rodrigues -- 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] 64-bit gromacs-4.0.7 for Mac OSX
J. Rui Rodrigues wrote: Dear all, With gromacs-4.0.5, one had the possibility to compile a 64-bit version of gromacs for Mac OS X using configure -- enable-apple-64bit. This was even suggested by configure to improve performance. With gromacs-4.0.7, the option --enable-apple-64bit of configure has disappeared and configure no longer suggests to compile in 64-bit. Is this no longer recommended for Mac OSX? This feature is auto-detected in version 4.0.7: http://www.gromacs.org/About_Gromacs/Release_Notes/Revisions_in_4.0 -Justin Thanks for your time, Rui Rodrigues -- 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] implicit solvent simulation in gromacs
Chanchal wrote: Hi All, I want to perform MD simulation of a protein in implicit solvent using gromacs 4.0.7. I looked into the manual but did not get any information regarding the implicit solvent. Is it avilable in gromacs? I searched in the mailing list and found someone in older mail said its not avilable. If it is avilable, could anybody please give me the mdp option. Is it okay to use 43a1 FF? It is not available. Implicit solvent has been implemented in the development code and is expected in the next release. I think I posted the same thing just yesterday... -Justin Thanks Chanchal -- 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] Re: g_wham giving flat free energy
Michael McGovern wrote: Hi everyone. I'm having some trouble using g_wham to analyze some results. I have some simulations from gromacs 3.3 using the pull code. I'm using the latest version of g_wham to analyze the results, which the help file says is ok, using the -ip option. I've gotten almost everything to work, and it generates histograms that seem perfectly reasonable, but sometimes the free energy it outputs is completely flat, with each bin having a free energy value of 0. I've played around with the -b and -e options using only part of my data, and sometimes it gives non-flat free energies, other times not. I see no logic to when it works and when it doesn't. My data does have good overlap of the histograms, and it sometimes converges even when I use data that have no overlaps, so that doesn't seem to be the problem. I'm completely confused. Does anyone know what could cause this? Hi Micheal, how large is your data? Could you send me a tar.gz of your pdo files? I would like to make sure that there is no bug in g_wham. Jochen I had this problem also when I tried to calculate dimerization free energies using umbrella sampling and g_wham. The problem seemed to occur every time I included .tpr files that contained configurations in which there were no more interaction between the previously dimerized set. What I mean is, when I monitored the LJ and Coul interactions between my molecules, I found out that there would be no more interaction beyond, lets say, 2.1 nm (distance between COM of my molecules). When I included the 2.0, 2.1, 2.2 nm etc windows in my g_wham analysis, I got a flat free energy graphic. Just wanted to add that to the post. Thanks -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests 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] implicit solvent simulation in gromacs
Implicit solvent are still not available in gromacs. Using 43a1 FF is fine, except with implicit solvent! Or you should have one compatible with it! On Apr 28, 2010, at 6:27 PM, Chanchal wrote: Hi All, I want to perform MD simulation of a protein in implicit solvent using gromacs 4.0.7. I looked into the manual but did not get any information regarding the implicit solvent. Is it avilable in gromacs? I searched in the mailing list and found someone in older mail said its not avilable. If it is avilable, could anybody please give me the mdp option. Is it okay to use 43a1 FF? Thanks Chanchal -- 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] 64-bit gromacs-4.0.7 for Mac OSX
Hi, So, there is something going wrong here... My machine: Mac OS X 10.5.8 with 2 x 3.2 GHz Quad-Core Intel Xeon -- Compilation of gromacs against fftw3 libs installed with fink (installed in /sw/; no 64-bit libs) goes fine, but results in 32-bit binaries: tar xvzf gromacs-4.0.7.tar.gz ; cd gromacs-4.0.7 ./configure CPPFLAGS=-I/sw/include LDFLAGS=-L/sw/lib --prefix=/usr/local/gromacs407 --program-suffix=407 make sudo make install file /usr/local/gromacs407/bin/grompp407 /usr/local/gromacs407/bin/grompp407: Mach-O executable i386 After removing the gromacs-4.0.7 folder and also /usr/local/gromacs407, I tried to compile gromacs against 64-bit fftw libs: -- Compilation of fftw3 64bit (installed in /usr/local/): tar xvzf fftw-3.2.2.tar.gz; cd fftw-3.2.2 ./configure --enable-float CFLAGS=-m64 make sudo make install -- Compilation of gromacs against 64-bit fftw libs tar xvzf gromacs-4.0.7.tar.gz ; cd gromacs-4.0.7 ./configure CPPFLAGS=-I/usr/local/include LDFLAGS=-L/usr/local/lib --prefix=/usr/local/gromacs407 --program-suffix=407 make This gives an error (see below). I don't see what I am doing wrong. Please note that compilation of gromacs-4.0.5 against these 64bit fftw libs is OK. Do you have any suggestion? Thanks for your time, Rui Rodrigues Output from make: = (...) /bin/sh ../../libtool --tag=CC --mode=link cc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -L/usr/local/lib - framework Accelerate -o grompp grompp.o libgmxpreprocess.la ../mdlib/libmd.la ../gmxlib/libgmx.la -lxml2 -L/usr/X11/lib -lfftw3f -lm -lSM -lICE -lX11 cc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -framework Accelerate -o grompp grompp.o -L/usr/local/lib ./.libs/libgmxpreprocess.a -L/usr/X11/lib ../mdlib/.libs/libmd.a /Users/jrui/Desktop/gromacs-4.0.7/src/gmxlib/.libs/libgmx.a ../gmxlib/.libs/libgmx.a /usr/lib/libxml2.dylib -lpthread -lz -licucore /usr/local/lib/libfftw3f.a -lm /usr/X11/lib/libSM.6.dylib /usr/X11/lib/libICE.6.dylib /usr/X11/lib/libX11.6.dylib /usr/X11/lib/libXau.6.dylib /usr/X11/lib/libXdmcp.6.dylib ld warning: in /usr/local/lib/libfftw3f.a, file is not of required architecture Undefined symbols: _fftwf_execute_dft, referenced from: _gmx_fft_1d in libmd.a(gmx_fft_fftw3.o) _gmx_fft_2d in libmd.a(gmx_fft_fftw3.o) _gmx_fft_3d in libmd.a(gmx_fft_fftw3.o) _fftwf_free, referenced from: _gmx_fft_destroy in libmd.a(gmx_fft_fftw3.o) _gmx_fft_init_1d in libmd.a(gmx_fft_fftw3.o) _gmx_fft_init_1d in libmd.a(gmx_fft_fftw3.o) _gmx_fft_init_1d in libmd.a(gmx_fft_fftw3.o) _gmx_fft_init_1d in libmd.a(gmx_fft_fftw3.o) _gmx_fft_init_1d in libmd.a(gmx_fft_fftw3.o) _gmx_fft_init_1d in libmd.a(gmx_fft_fftw3.o) _gmx_fft_init_1d in libmd.a(gmx_fft_fftw3.o) _gmx_fft_init_1d_real in libmd.a(gmx_fft_fftw3.o) _gmx_fft_init_1d_real in libmd.a(gmx_fft_fftw3.o) _gmx_fft_init_1d_real in libmd.a(gmx_fft_fftw3.o) _gmx_fft_init_1d_real in libmd.a(gmx_fft_fftw3.o) _gmx_fft_init_1d_real in libmd.a(gmx_fft_fftw3.o) _gmx_fft_init_1d_real in libmd.a(gmx_fft_fftw3.o) _gmx_fft_init_1d_real in libmd.a(gmx_fft_fftw3.o) _gmx_fft_init_2d in libmd.a(gmx_fft_fftw3.o) _gmx_fft_init_2d in libmd.a(gmx_fft_fftw3.o) _gmx_fft_init_2d in libmd.a(gmx_fft_fftw3.o) _gmx_fft_init_2d in libmd.a(gmx_fft_fftw3.o) _gmx_fft_init_2d in libmd.a(gmx_fft_fftw3.o) _gmx_fft_init_2d in libmd.a(gmx_fft_fftw3.o) _gmx_fft_init_2d in libmd.a(gmx_fft_fftw3.o) _gmx_fft_init_2d_real in libmd.a(gmx_fft_fftw3.o) _gmx_fft_init_2d_real in libmd.a(gmx_fft_fftw3.o) _gmx_fft_init_2d_real in libmd.a(gmx_fft_fftw3.o) _gmx_fft_init_2d_real in libmd.a(gmx_fft_fftw3.o) _gmx_fft_init_2d_real in libmd.a(gmx_fft_fftw3.o) _gmx_fft_init_2d_real in libmd.a(gmx_fft_fftw3.o) _gmx_fft_init_2d_real in libmd.a(gmx_fft_fftw3.o) _gmx_fft_init_3d in libmd.a(gmx_fft_fftw3.o) _gmx_fft_init_3d in libmd.a(gmx_fft_fftw3.o) _gmx_fft_init_3d in libmd.a(gmx_fft_fftw3.o) _gmx_fft_init_3d in libmd.a(gmx_fft_fftw3.o) _gmx_fft_init_3d in libmd.a(gmx_fft_fftw3.o) _gmx_fft_init_3d in libmd.a(gmx_fft_fftw3.o) _gmx_fft_init_3d in libmd.a(gmx_fft_fftw3.o) _gmx_fft_init_3d_real in libmd.a(gmx_fft_fftw3.o) _gmx_fft_init_3d_real in libmd.a(gmx_fft_fftw3.o) _gmx_fft_init_3d_real in libmd.a(gmx_fft_fftw3.o) _gmx_fft_init_3d_real in libmd.a(gmx_fft_fftw3.o) _gmx_fft_init_3d_real in libmd.a(gmx_fft_fftw3.o) _gmx_fft_init_3d_real in libmd.a(gmx_fft_fftw3.o) _gmx_fft_init_3d_real in libmd.a(gmx_fft_fftw3.o) _fftwf_execute_dft_c2r, referenced from: _gmx_fft_1d_real in libmd.a(gmx_fft_fftw3.o) _gmx_fft_2d_real in libmd.a(gmx_fft_fftw3.o) _gmx_fft_3d_real in libmd.a(gmx_fft_fftw3.o) _fftwf_plan_dft_1d, referenced from:
[gmx-users] g_wham gets stuck
Hi All, I have some problems with g_wham, and i already gone through all the postings and didn't find a hint.. basically, I'm trying to calculate PMF between two charged plates. I've performed a pulling simulation between the 2 plates according to Justin's UMBRELLA tutorial in the website (all steps, i.e., minimization, equilibration etc. up to that point work fine) from the pulling i generated input configurations for the umbrella sampling runs (pull=umbrella , rate=0.0), which are 15 ns long and collected all the output pullf.xvg and *.tpr files. i then run g_wham (with -it and -if) and it works fine at the beginning, but then the computer simply gets stuck (!?) and the calculation is killed - with no error massage. what is it that I'm doing wrong? it looks like my output data (pullf and tpr files) are fine, but is it possible that some of them causing the problem? this is really frustrating.. need your help, Amir -- 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] g_wham gets stuck
Amir Marcovitz wrote: Hi All, I have some problems with g_wham, and i already gone through all the postings and didn't find a hint.. For problems like these (which are hard to diagnose!), your Gromacs version, compilers used, OS, etc. would be useful. basically, I'm trying to calculate PMF between two charged plates. I've performed a pulling simulation between the 2 plates according to Justin's UMBRELLA tutorial in the website (all steps, i.e., minimization, equilibration etc. up to that point work fine) from the pulling i generated input configurations for the umbrella sampling runs (pull=umbrella , rate=0.0), which are 15 ns long and collected all the output pullf.xvg and *.tpr files. i then run g_wham (with -it and -if) and it works fine at the beginning, A real command line would be better. Does g_wham report reading in all of the files correctly? but then the computer simply gets stuck (!?) and the calculation is killed - with no error massage. what is it that I'm doing wrong? Not a clue, based on what you've provided. Sounds like a reasonable procedure to me. it looks like my output data (pullf and tpr files) are fine, but is it possible that some of them causing the problem? Are your input files (.dat) intact? In the appropriate order, etc? Are all your file names unique? Additional details like these would be good. You can also add the -debug flag to get a .log file of what g_wham is doing. That might be useful. -Justin this is really frustrating.. need your help, Amir -- 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] pull distance
Dear Gromacs Users I have set my pull option as constant force and the pull geometry is distance the manual has stated that the pull_k1 unit is kJ/mol/nm . does it mean that the force applied to the protein is proportional to the distance between the 2 groups ? else what is it ? my second question is that what is the preferable choice for the pull ref group (pull_group0) in a protein when the force is exerted to the first and last res of the molecule . Best Regards Ali -- 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] angle
Hello, I am doing solvation of glucose. I am trying to calculate a angle between three selected carbon atoms. If I run g_angle using angle.ndx file it consider all carbon atom. In force field C-C-C 112.5 is specified so its making a group of all carbon atoms. I am interested in selected carbon atoms. How can I plot an angle of selected three carbon atoms? Thanks Nilesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests 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] angle
Nilesh Dhumal wrote: Hello, I am doing solvation of glucose. I am trying to calculate a angle between three selected carbon atoms. If I run g_angle using angle.ndx file it consider all carbon atom. In force field C-C-C 112.5 is specified so it’s making a group of all carbon atoms. I am interested in selected carbon atoms. How can I plot an angle of selected three carbon atoms? Make an appropriate index group, which it doesn't sound like you've done. If there's a specific angle you want to measure, you don't even necessarily need make_ndx, just write the group using a text editor with the appropriate atom numbers. -Justin Thanks Nilesh -- 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] 64-bit gromacs-4.0.7 for Mac OSX
On 29/04/2010 5:22 AM, J. Rui Rodrigues wrote: Hi, So, there is something going wrong here... My machine: Mac OS X 10.5.8 with 2 x 3.2 GHz Quad-Core Intel Xeon -- Compilation of gromacs against fftw3 libs installed with fink (installed in /sw/; no 64-bit libs) goes fine, but results in 32-bit binaries: tar xvzf gromacs-4.0.7.tar.gz ; cd gromacs-4.0.7 ./configure CPPFLAGS=-I/sw/include LDFLAGS=-L/sw/lib --prefix=/usr/local/gromacs407 --program-suffix=407 make sudo make install file /usr/local/gromacs407/bin/grompp407 /usr/local/gromacs407/bin/grompp407: Mach-O executable i386 After removing the gromacs-4.0.7 folder and also /usr/local/gromacs407, I tried to compile gromacs against 64-bit fftw libs: -- Compilation of fftw3 64bit (installed in /usr/local/): tar xvzf fftw-3.2.2.tar.gz; cd fftw-3.2.2 ./configure --enable-float CFLAGS=-m64 make sudo make install -- Compilation of gromacs against 64-bit fftw libs tar xvzf gromacs-4.0.7.tar.gz ; cd gromacs-4.0.7 ./configure CPPFLAGS=-I/usr/local/include LDFLAGS=-L/usr/local/lib --prefix=/usr/local/gromacs407 --program-suffix=407 make This gives an error (see below). I don't see what I am doing wrong. It looks fine. Please note that compilation of gromacs-4.0.5 against these 64bit fftw libs is OK. Do you have any suggestion? Thanks for your time, Rui Rodrigues Output from make: = (...) /bin/sh ../../libtool --tag=CC --mode=link cc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -L/usr/local/lib - framework Accelerate -o grompp grompp.o libgmxpreprocess.la ../mdlib/libmd.la ../gmxlib/libgmx.la -lxml2 -L/usr/X11/lib -lfftw3f -lm -lSM -lICE -lX11 cc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -framework Accelerate -o grompp grompp.o -L/usr/local/lib ./.libs/libgmxpreprocess.a -L/usr/X11/lib ../mdlib/.libs/libmd.a /Users/jrui/Desktop/gromacs-4.0.7/src/gmxlib/.libs/libgmx.a ../gmxlib/.libs/libgmx.a /usr/lib/libxml2.dylib -lpthread -lz -licucore /usr/local/lib/libfftw3f.a -lm /usr/X11/lib/libSM.6.dylib /usr/X11/lib/libICE.6.dylib /usr/X11/lib/libX11.6.dylib /usr/X11/lib/libXau.6.dylib /usr/X11/lib/libXdmcp.6.dylib ld warning: in /usr/local/lib/libfftw3f.a, file is not of required architecture What does (e.g.) nm /usr/local/lib/libfftw3f.a have to say? Also, look at ls -l /usr/local/lib/libfftw* to see whether you're picking up versions with the timestamps you expect... Maybe your FFTW configuration only installed dynamic libraries, or something. I don't know why compiling 4.0.5 would have succeeded, however. Mark Undefined symbols: _fftwf_execute_dft, referenced from: _gmx_fft_1d in libmd.a(gmx_fft_fftw3.o) _gmx_fft_2d in libmd.a(gmx_fft_fftw3.o) _gmx_fft_3d in libmd.a(gmx_fft_fftw3.o) _fftwf_free, referenced from: _gmx_fft_destroy in libmd.a(gmx_fft_fftw3.o) _gmx_fft_init_1d in libmd.a(gmx_fft_fftw3.o) _gmx_fft_init_1d in libmd.a(gmx_fft_fftw3.o) _gmx_fft_init_1d in libmd.a(gmx_fft_fftw3.o) _gmx_fft_init_1d in libmd.a(gmx_fft_fftw3.o) _gmx_fft_init_1d in libmd.a(gmx_fft_fftw3.o) _gmx_fft_init_1d in libmd.a(gmx_fft_fftw3.o) _gmx_fft_init_1d in libmd.a(gmx_fft_fftw3.o) _gmx_fft_init_1d_real in libmd.a(gmx_fft_fftw3.o) _gmx_fft_init_1d_real in libmd.a(gmx_fft_fftw3.o) _gmx_fft_init_1d_real in libmd.a(gmx_fft_fftw3.o) _gmx_fft_init_1d_real in libmd.a(gmx_fft_fftw3.o) _gmx_fft_init_1d_real in libmd.a(gmx_fft_fftw3.o) _gmx_fft_init_1d_real in libmd.a(gmx_fft_fftw3.o) _gmx_fft_init_1d_real in libmd.a(gmx_fft_fftw3.o) _gmx_fft_init_2d in libmd.a(gmx_fft_fftw3.o) _gmx_fft_init_2d in libmd.a(gmx_fft_fftw3.o) _gmx_fft_init_2d in libmd.a(gmx_fft_fftw3.o) _gmx_fft_init_2d in libmd.a(gmx_fft_fftw3.o) _gmx_fft_init_2d in libmd.a(gmx_fft_fftw3.o) _gmx_fft_init_2d in libmd.a(gmx_fft_fftw3.o) _gmx_fft_init_2d in libmd.a(gmx_fft_fftw3.o) _gmx_fft_init_2d_real in libmd.a(gmx_fft_fftw3.o) _gmx_fft_init_2d_real in libmd.a(gmx_fft_fftw3.o) _gmx_fft_init_2d_real in libmd.a(gmx_fft_fftw3.o) _gmx_fft_init_2d_real in libmd.a(gmx_fft_fftw3.o) _gmx_fft_init_2d_real in libmd.a(gmx_fft_fftw3.o) _gmx_fft_init_2d_real in libmd.a(gmx_fft_fftw3.o) _gmx_fft_init_2d_real in libmd.a(gmx_fft_fftw3.o) _gmx_fft_init_3d in libmd.a(gmx_fft_fftw3.o) _gmx_fft_init_3d in libmd.a(gmx_fft_fftw3.o) _gmx_fft_init_3d in libmd.a(gmx_fft_fftw3.o) _gmx_fft_init_3d in libmd.a(gmx_fft_fftw3.o) _gmx_fft_init_3d in libmd.a(gmx_fft_fftw3.o) _gmx_fft_init_3d in libmd.a(gmx_fft_fftw3.o) _gmx_fft_init_3d in libmd.a(gmx_fft_fftw3.o) _gmx_fft_init_3d_real in libmd.a(gmx_fft_fftw3.o) _gmx_fft_init_3d_real in libmd.a(gmx_fft_fftw3.o) _gmx_fft_init_3d_real in libmd.a(gmx_fft_fftw3.o)
[gmx-users] Lincs warning
Dear gmx experts, I am having problem doing MD run for a hydrocarbon system. The system contains a stack of Hexane molecules using editconf. The distance between molecuels in the box is more than 30 A. I am wondering why I get large forces (system is blowing up) with this distance!. (LINCS warning) with dt=0.002 Program mdrun, VERSION 4.0.7 Source code file: constr.c, line: 136 Fatal error: Too many LINCS warnings (1053) If you know what you are doing you can adjust the lincs warning threshold in your mdp file or set the environment variable GMX_MAXCONSTRWARN to -1, but normally it is better to fix the problem It seems Fmax, Epot values are reasonable. . In the list archive I read this statement by Mr.Justin Lemskul: changing cutoffs haphazardly is a recipe for failure but I have no idea how this works* * I also reduced the timestep to 0.001 ps but it did not work. I even did not get those written pdb files I got from dt=0.002 I had a look at structures and they were like rings!!. (initially hezane had a linear structure). Thank you for your time and help in advance *em output file:* Steepest Descents: Tolerance (Fmax) = 1.0e+03 Number of steps= 100 Step=0, Dmax= 1.0e-02 nm, Epot= 8.36824e+05 Fmax= 2.26627e+03, atom= 2947 Step=1, Dmax= 1.0e-02 nm, Epot= 8.17823e+05 Fmax= 2.98349e+03, atom= 2007 Step=2, Dmax= 1.2e-02 nm, Epot= 7.87850e+05 Fmax= 2.24621e+03, atom= 2447 Step=3, Dmax= 1.4e-02 nm, Epot= 7.70259e+05 Fmax= 3.13292e+03, atom= 3127 Step=4, Dmax= 1.7e-02 nm, Epot= 7.50886e+05 Fmax= 2.87650e+03, atom= 3125 Step=5, Dmax= 2.1e-02 nm, Epot= 7.15803e+05 Fmax= 5.48652e+03, atom= 3127 Step=6, Dmax= 2.5e-02 nm, Epot= 6.59011e+05 Fmax= 2.97146e+03, atom= 3105 Step=7, Dmax= 3.0e-02 nm, Epot= 7.10849e+05 Fmax= 5.51243e+03, atom= 3127^MStep=8, Dmax= 1.5e-02 nm, Epot= 6.38805e+05 Fmax= 3.87761e+03, atom= 3107 Step=9, Dmax= 1.8e-02 nm, Epot= 6.21481e+05 Fmax= 2.69101e+03, atom= 1687 Step= 10, Dmax= 2.1e-02 nm, Epot= 6.43071e+05 Fmax= 5.74780e+03, atom= 227^MStep= 11, Dmax= 1.1e-02 nm, Epot= 6.00633e+05 Fmax= 2.56262e+03, atom= 3107 Step= 12, Dmax= 1.3e-02 nm, Epot= 5.86914e+05 Fmax= 2.40254e+03, atom= 1687 Step= 13, Dmax= 1.5e-02 nm, Epot= 5.85431e+05 Fmax= 4.58696e+03, atom= 3107 Step= 14, Dmax= 1.9e-02 nm, Epot= 5.61423e+05 Fmax= 2.94308e+03, atom= 3127 Step= 15, Dmax= 2.2e-02 nm, Epot= 5.85550e+05 Fmax= 5.56128e+03, atom= 1827^MStep= 16, Dmax= 1.1e-02 nm, Epot= 5.43780e+05 Fmax= 1.91577e+03, atom= 3107 Step= 17, Dmax= 1.3e-02 nm, Epot= 5.42825e+05 Fmax= 3.49456e+03, atom= 4247 Step= 18, Dmax= 1.6e-02 nm, Epot= 5.30046e+05 Fmax= 3.16969e+03, atom= 4247 Step= 19, Dmax= 1.9e-02 nm, Epot= 5.41307e+05 Fmax= 4.27646e+03, atom= 4247^MStep= 20, Dmax= 9.6e-03 nm, Epot= 5.14493e+05 Fmax= 1.28031e+03, atom= 3115 Step= 21, Dmax= 1.2e-02 nm, Epot= 5.14984e+05 Fmax= 3.45692e+03, atom= 4247^MStep= 22, Dmax= 5.8e-03 nm, Epot= 5.07865e+05 Fmax= 1.27065e+03, atom= 3115 Step= 23, Dmax= 6.9e-03 nm, Epot= 5.02771e+05 Fmax= 1.75304e+03, atom= 4247 Step= 24, Dmax= 8.3e-03 nm, Epot= 4.98096e+05 Fmax= 2.10118e+03, atom= 4247Step= 23, Dmax= 6.9e-03 nm, Epot= 5.02771e+05 Fmax= 1.75304e+03, atom= 4247 Step= 24, Dmax= 8.3e-03 nm, Epot= 4.98096e+05 Fmax= 2.10118e+03, atom= 4247 Step= 25, Dmax= 1.0e-02 nm, Epot= 4.95017e+05 Fmax= 2.30502e+03, atom= 4247 Step= 26, Dmax= 1.2e-02 nm, Epot= 4.94561e+05 Fmax= 3.17535e+03, atom= 1847 Step= 27, Dmax= 1.4e-02 nm, Epot= 4.91526e+05 Fmax= 2.99909e+03, atom= 1847 Step= 28, Dmax= 1.7e-02 nm, Epot= 5.00763e+05 Fmax= 4.45550e+03, atom= 1847^MStep= 29, Dmax= 8.6e-03 nm, Epot= 4.76093e+05 Fmax= 9.86600e+02, atom= 3115 writing lowest energy coordinates. Steepest Descents converged to Fmax 1000 in 30 steps Potential Energy = 4.76092783832156e+05 Maximum force = 9.86600079729483e+02 on atom 3115 Norm of force = 5.33725886931530e+02 gcq#345: Look at these, my work-strong arms (P.J. Harvey) md parameter file: title = Hexane cpp = /lib/cpp ;Preprocessing define = -DPOSRES ;Run control integrator = md dt = 0.001; ps ! nsteps = 5000; total 1.0 ps. nstcomm = 1; frequency for center of mass motion removal ;Output control nstenergy = 10; frequency to write energies to energy file. i.e., energies and other statistical data are stored every 10 steps nstxout = 10; frequency to write coordinates/velocity/force to output trajectory file nstvout = 1000 nstfout = 1 ;nstlog = 10; frequency to write energies to log file ;Neighbor searching nstlist = 10; neighborlist will be updated at least every 10 steps ;ns_type = grid ;Electrostatics/VdW coulombtype =
Re: [gmx-users] Lincs warning
Moeed wrote: Dear gmx experts, I am having problem doing MD run for a hydrocarbon system. The system contains a stack of Hexane molecules using editconf. The distance between molecuels in the box is more than 30 A. I am wondering why I get large forces (system is blowing up) with this distance!. (LINCS warning) with dt=0.002 Program mdrun, VERSION 4.0.7 Source code file: constr.c, line: 136 Fatal error: Too many LINCS warnings (1053) If you know what you are doing you can adjust the lincs warning threshold in your mdp file or set the environment variable GMX_MAXCONSTRWARN to -1, but normally it is better to fix the problem It seems Fmax, Epot values are reasonable. . In the list archive I read I would say they are not. snip Steepest Descents converged to Fmax 1000 in 30 steps Potential Energy = 4.76092783832156e+05 Maximum force = 9.86600079729483e+02 on atom 3115 Norm of force = 5.33725886931530e+02 You have a reasonable force, but your potential energy is large and positive, indicative strong repulsive forces in your system. snip define = -DPOSRES What are you restraining, and what purpose does it serve? -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] Freezing a portion of a protein during simulation
Hello Justin, Thanks a lot for your reply. I am using the option freezegrps in my .mdp file, given below: - ;define = -DSTRONG_POSRES define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md; leap-frog integrator nsteps = 1 ; 2 * 5 = 100 ps dt = 0.002 ; 2 fs ; Output control nstxout = 100 ; save coordinates every 0.2 ps nstvout = 100 ; save velocities every 0.2 ps nstenergy = 100 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps ; Bond parameters continuation= no; first dynamics run constraint_algorithm = lincs; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cels nstlist = 5 ; 10 fs rlist = 1.0 ; short-range neighborlist cutoff (in nm) rcoulomb= 1.0 ; short-range electrostatic cutoff (in nm) rvdw= 1.0 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Protein Non-Protein ; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 300 300 ; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = no; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp= 300 ; temperature for Maxwell distribution gen_seed= -1; generate a random seed freezegrps = Fixed freezedim = Y Y Y I was just wondering how to give the energygrp_excl parameters with it. Can you please guide me regarding this and also please go through the other parameters in the .mdp file. Regards, Anirban On Wed, Apr 28, 2010 at 4:52 PM, Justin A. Lemkul jalem...@vt.edu wrote: Anirban Ghosh wrote: Hello Justin, In my topology file I am declaring: --- ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Strong position restraints on rest of B2AR #ifdef STRONG_POSRES #include strong_posre.itp #endif What is in strong_posre.itp? Presumably you're only restraining certain residues, right? Did you create this with genrestr and an appropriate index group? ; Include water topology #include spc.itp - And in my .mdp file I am giving: - define = -DSTRONG_POSRES; Run parameters integrator = md; leap-frog integrator nsteps = 5000 ; 2 * 5 = 100 ps dt = 0.002 ; 2 fs --- If this is the entirety of your .mdp file, you're asking for trouble. Allowing all other parameters to be taken as default is very dangerous, and probably inappropriate (most notably cutoff electrostatics). But now what I am getting is that if I run MD using these restraints on the helical portion of the protein, then I am getting LINCS errors. However, if I allow the entire protein to move during MD, then it is running fine. What mistake am I making? And how can I freeze properly the helical portions and simulate only the loop? Thanks a lot in advance. Recognize that there is a difference between freezing and restraining. Read in the manual about what freezing is versus position restraints. Either way, you should be able to get things up and running, but position restraints are a bit easier to implement. If an unrestrained simulation runs fine (using that fragmented .mdp file?)
