[gmx-users] How to change the resname?
Hello, first, I make a grateful acknowledgement for Mark and Justin's help to guide me to install the gromacs,I have installed it well. I have another question need you help , could I change the resname in the .gro and .top or .itp documents? if yes, how shall I do, just change it ? 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
[gmx-users] Re: charmm lipid simulation and vsites
Hello David, I send answer to the gromacs mailing list also. 12 apr 2010 kl. 17.51 skrev David Caplan: > I am still experimenting with the CHARMM27 support in Gromacs. I am > using a very recent git version (from last week). > > Currently, I'm trying to equilibrate a membrane bilayer with virtual > sites. The membrane is DPPC with the Sonne et al. parameters (for zero > surface tension): > Sonne et al. Reparameterization of all-atom > dipalmitoylphosphatidylcholine lipid parameters enables simulation of > fluid bilayers at zero tension. Biophys J (2007) vol. 92 (12) pp. > 4157-67 > > I am not so familiar with vsites, but I have read the documentation > and I saw you used vsites in your recent paper. Have you used vsites > with membrane simulations using CHARMM27? No, I have not but it should be straight forward. > If so, what kind of pressure > coupling do you use? is any surface tension applied? > If you have an example MDP that you used for this I would love to take > a look at it. I would use semiisotropic Berendsen for equilibration and perhaps switch to Parrinello-Rahman during production but when it comes to surface tension and CHARMM simulations I'm afraid I don't have any experience. Guess you have to read the cited paper carefully to figure this out. > > Also, do you typically run your CHARMM27 simulations using Langevin dynamics? No, not when you have explicit solvent. /Pär -- 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] Amino acid simulation
Thanks Justin. It worked perfectly. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Tue, Apr 13, 2010 at 1:08 AM, Justin A. Lemkul wrote: > > > Chandan Choudhury wrote: > >> Hello gmx-users >> >> I am trying to simulate an amino acid (say GLN). It can be as a >> zwitterionic form or uncharged ends. Neither ffamber or ffopls force fields >> has a complete parameter for them. While in ffamber, I have the >> > > This is not true. OPLS can handle isolated amino acids, you just have to > manually choose the termini in pdb2gmx (using -ter). Use the "zwitterion" > forms of the termini, since in fact, you have a zwitterion. > > -Justin > > > parameters for CGLU and NGLU, but not for a Glutamine. Do I need to define >> it there, or there is some way out. If I need to define it, how do I retrive >> the partial charges. >> >> Any insight would be very helpful. >> Thanks >> >> Chandan >> >> -- >> Chandan kumar Choudhury >> NCL, Pune >> INDIA >> >> > -- > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Segmentation fault with g_order
Hello I tried to run g_order on a cluster with Core 2 Quad Q6600 processor where the Gromacs Suite 4.0.1 has been compiled in single precision. The program stops with a message from the compiler (i.e. in Spanish): "Violación de segmento" (=Segmentation fault, I guess) and I couldn't find an answer neither in the manual nor in the web. The program is run with default parameters on a simulation of a membrane (the index.ndx contains the membrane and the waters). Below, you can find the output. Could someone give a clue about the problem and what to do? Thanks a lot for your help. -- -- :-) g_order (-: Option Filename Type Description -f traj.xtc InputTrajectory: xtc trr trj gro g96 pdb cpt -n index.ndx InputIndex file -s topol.tpr InputRun input file: tpr tpb tpa -o order.xvg Output xvgr/xmgr file -od deuter.xvg Output xvgr/xmgr file -os sliced.xvg Output xvgr/xmgr file -Sg sg-ang.xvg Output, Opt. xvgr/xmgr file -Sksk-dist.xvg Output, Opt. xvgr/xmgr file Option Type Value Description -- -[no]h bool no Print help info and quit -niceint19 Set the nicelevel -b time 0 First frame (ps) to read from trajectory -e time 0 Last frame (ps) to read from trajectory -dt time 0 Only use frame when t MOD dt = first time (ps) -[no]w bool no View output xvg, xpm, eps and pdb files -[no]xvgrbool yes Add specific codes (legends etc.) in the output xvg files for the xmgrace program -d enum z Direction of the normal on the membrane: z, x or y -sl int1 Calculate order parameter as function of boxlength, dividing the box in #nr slices. -[no]szonly bool no Only give Sz element of order tensor. (axis can be specified with -d) -[no]unsat bool no Calculate order parameters for unsaturated carbons. Note that this cannot be mixed with normal order parameters. Taking z axis as normal to the membrane Reading file topol.tpr, VERSION 4.0.7 (single precision) Using following groups: Groupname: DMPC First atomname: C33 First atomnr 0 Groupname: SOL First atomname: OW First atomnr 5888 Reading frame 0 time0.000 Number of elements in first group: 5888 Reading frame 1 time0.500 Violación de segmento --- -- Javier CEREZO BASTIDA - Dpto. Química-Física Universidad de Murcia 30100 Murcia (SPAIN) Tlf.(+34)868887434 -- 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 prepare the two tolopogy files when doing TI calculation?
Dear GMX users, I want to do some TI calculation using GMX, and I have learned the tutorial of TI calculation from this web site http://www.dillgroup.ucsf.edu/group/wiki/index.php/Free_Energy:_Tutorial. So I have know how to run TI calculations. But there is still a problem. I don't know how to prepare the two topology files, which are initial and final states, respectively. Could somebody give me some suggestion on it? Any response will be highly appreciated! Thanks! All the best, Qinghua -- 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: Regarding Error "Atomtype OS not found"
> Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp > Generated 837 of the 2346 non-bonded parameter combinations > --- > Program grompp, VERSION 4.0.5 > Source code file: toppush.c, line: 947 > Fatal error: > Atomtype OS not found > > Can anyone help me to solve this problem? > > Any kind of help is highly appreciable. Post your "ff_dum.itp" here. -- Dr. Vitaly Chaban http://chaban.at.ua -- 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] Segmentation fault with g_order
Javier Cerezo wrote: Hello I tried to run g_order on a cluster with Core 2 Quad Q6600 processor where the Gromacs Suite 4.0.1 has been compiled in single precision. The program stops with a message from the compiler (i.e. in Spanish): "Violación de segmento" (=Segmentation fault, I guess) and I couldn't find an answer neither in the manual nor in the web. The program is run with default parameters on a simulation of a membrane (the index.ndx contains the membrane and the waters). Below, you can find the output. Could someone give a clue about the problem and what to do? Your index file is wrong. See here: http://www.gromacs.org/Documentation/Gromacs_Utilities/g_order -Justin Thanks a lot for your help. -- -- :-) g_order (-: Option Filename Type Description -f traj.xtc InputTrajectory: xtc trr trj gro g96 pdb cpt -n index.ndx InputIndex file -s topol.tpr InputRun input file: tpr tpb tpa -o order.xvg Output xvgr/xmgr file -od deuter.xvg Output xvgr/xmgr file -os sliced.xvg Output xvgr/xmgr file -Sg sg-ang.xvg Output, Opt. xvgr/xmgr file -Sksk-dist.xvg Output, Opt. xvgr/xmgr file Option Type Value Description -- -[no]h bool no Print help info and quit -niceint 19 Set the nicelevel-b time 0 First frame (ps) to read from trajectory -e time 0 Last frame (ps) to read from trajectory -dt time 0 Only use frame when t MOD dt = first time (ps) -[no]w bool no View output xvg, xpm, eps and pdb files -[no]xvgrbool yes Add specific codes (legends etc.) in the output xvg files for the xmgrace program -d enum z Direction of the normal on the membrane: z, x or y -sl int1 Calculate order parameter as function ofboxlength, dividing the box in #nr slices. -[no]szonly bool no Only give Sz element of order tensor. (axis can be specified with -d)-[no]unsat bool no Calculate order parameters for unsaturated carbons. Note that this cannot be mixed with normal order parameters. Taking z axis as normal to the membrane Reading file topol.tpr, VERSION 4.0.7 (single precision) Using following groups:Groupname: DMPC First atomname: C33 First atomnr 0 Groupname: SOL First atomname: OW First atomnr 5888 Reading frame 0 time0.000 Number of elements in first group: 5888 Reading frame 1 time0.500 Violación de segmento --- -- 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] How to change the resname?
kecy...@sina.com wrote: Hello, first, I make a grateful acknowledgement for Mark and Justin's help to guide me to install the gromacs,I have installed it well. I have another question need you help , could I change the resname in the .gro and .top or .itp documents? if yes, how shall I do, just change it ? Yes, but I don't understand why you need/want to do this. -Justin Thank you ! -- 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] Fwd: small help
Dear Satish, you'll find more help in the mailing list of GROMACS. regarding the use of g_rmsdist, the option -h is very useful ... you can access single residues or subpart of a system by using and index. XAvier. Begin forwarded message: From: satish kumar ainala Date: April 13, 2010 12:14:17 PM GMT+02:00 To: x.peri...@rug.nl Subject: small help Dear sir, I am satish kumar persueing M.Sc Bioinfromatics from pondicherry university(INDIA). I have struck with a small command i need ur help to complete this procedure. Syntax for - g_rmsdist command for a single residue i want an example how to use this command for generating rmsd for a single flexible residue.. Plz help me sir in this regard..Thanking You . Yours Obediently , Satish kumar -- 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: Regarding Error "Atomtype OS not found"
Vitaly V. Chaban wrote: Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp Generated 837 of the 2346 non-bonded parameter combinations --- Program grompp, VERSION 4.0.5 Source code file: toppush.c, line: 947 Fatal error: Atomtype OS not found Can anyone help me to solve this problem? Any kind of help is highly appreciable. Post your "ff_dum.itp" here. Since ff_dum.itp is always read in by grompp, unless it has been severely hacked (which is possible), it is more likely that there is some inappropriate mixing of force fields going on here, like including a ligand topology that doesn't match the force field applied to the rest of the system. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_sas to calculate the n-hexane/water interface surface area
Hi all, I have a question regarding the g_sas command. Let's say I have an n-hexane/water interface. I want to calculate the accessible area between these two media. If I were to choose the calculation group as the 'system', and the output group as 'hexane' then, it should give me that area? Regards -- Ozge Engin ★☆ -- 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 prepare the two tolopogy files when doing TI calculation?
On 13/04/2010 7:35 PM, fancy2012 wrote: Dear GMX users, I want to do some TI calculation using GMX, and I have learned the tutorial of TI calculation from this web site http://www.dillgroup.ucsf.edu/group/wiki/index.php/Free_Energy:_Tutorial. So I have know how to run TI calculations. But there is still a problem. I don't know how to prepare the two topology files, which are initial and final states, respectively. Could somebody give me some suggestion on it? Any response will be highly appreciated! Thanks! Didn't the tutorial go through that? Look at its examples. 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] OpenMM
Hi all, I'm using the Application Programming Interface openMM for executing molecular dynamics simulations with Gromacs on an NVIDIA GTX 295 GPU (here is installed CUDA SDK for issuing and managing computations on GPU). Even if I have followed all the instructions reported for the correct installation of GPU, CUDA, OpenMM and even if my .mdp file for the simulation is written following the features supported in the release Gromacs-OpenMM, the output of the serial code running on CPU is quite different from that of the parallel code running on GPU (.gro files). Looking at the .log file I have also noticed that the energy terms 'Angle', 'Proper Dih.''Ryckaert-Bell.','LJ-14'Coulomb-14', 'LJ (SR)', 'Coulomb (SR), 'RF excl', are null for the simulation performed with the parallel code. I obtained these results during different simulations on several .pdb files. I used, for example, '1AKI.pdb' file, downloaded from the Protein Data Bank. I decided to choose ffamber94 force-field (even if this is more suitable for nucleic acids) and I treated the structure with an energy minimization of 1 ps and a position restraint of 5 ps. After these, I executed the md simulation using the following .mdp file as input for the mdrun-openmm program: cpp = /lib/cpp include = -I../top integrator = md dt = 0.002 nsteps = 1 nstlist = 5 ns_type = grid rlist= 1.2 pbc = xyz coulombtype = Reaction-Field rcoulomb = 1.2 vdwtype = switch rvdw_switch = 1.0 rvdw = 1.1 tcoupl = no Pcoupl = no gen_vel = no constraints = all-bonds I have performed a lot of simulations using even different options for the .mdp file (coulombtype, pbc...), but I have never obtained the expected results. Someone can help me? Thanks a lot, Giulia -- 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: Regarding Error "Atom type OS not found"
Dear Mark, I have used following .top file. ; Include forcefield parameters #include "ffG53a6.itp" #include "drg.itp" [ moleculetype ] ; Namenrexcl Protein_X 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeBchargeB massB 1 NL 1SER N 1 0.12914.0067 ; qtot 0.129 2 H 1SER H1 1 0.248 1.008 ; qtot 0.377 -- ; Include Position restraint file #ifdef POSRES #include "posre.itp" #endif ; Strong position restraints for InflateGRO #ifdef STRONG_POSRES #include "strong_posre.itp" #endif ;Include ligand topology ;#include "drg.itp" ; Include water topology #include "spc.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include generic topology for ions #include "ions.itp" [ system ] ; Name Protein [ molecules ] ; Compound#mols Protein_X 1 yoh1 Thanking you in anticipation. On 13/04/2010 1:49 PM, Jignesh Patel wrote: > Hello, > > while I am running grompp command, I am getting following error. > > Opening library file /usr/local/gromacs/share/ gromacs/top/ff_dum.itp > Generated 837 of the 2346 non-bonded parameter combinations > --- > Program grompp, VERSION 4.0.5 > Source code file: toppush.c, line: 947 > Fatal error: > Atomtype OS not found > > Can anyone help me to solve this problem? Yep, they can point out that atom type OS is not found. Since at this stage only you know about your topology and system preparation, and more particularly why you're trying to #include "ff_dum.itp", only you can reason why. Perhaps sharing some more detail will help... Mark -- Best Wishes, Jignesh Patel Pharmacoinformatics, NIPER -- 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: Regarding Error "Atom type OS not found"
Jignesh Patel wrote: Dear Mark, I have used following .top file. ; Include forcefield parameters #include "ffG53a6.itp" #include "drg.itp" Let me guess, drg.itp is from PRODRG? Then you probably have ffgmx atom types (like "OS") that are not supported by G53a6. Thus you are mixing force fields and generating an inconsistent physical model. There is PRODRG beta (2.5) that generates G96-compatible topologies, but the usual caveats about their accuracy apply :) -Justin [ moleculetype ] ; Namenrexcl Protein_X 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeBchargeB massB 1 NL 1SER N 1 0.12914.0067 ; qtot 0.129 2 H 1SER H1 1 0.248 1.008 ; qtot 0.377 -- ; Include Position restraint file #ifdef POSRES #include "posre.itp" #endif ; Strong position restraints for InflateGRO #ifdef STRONG_POSRES #include "strong_posre.itp" #endif ;Include ligand topology ;#include "drg.itp" ; Include water topology #include "spc.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include generic topology for ions #include "ions.itp" [ system ] ; Name Protein [ molecules ] ; Compound#mols Protein_X 1 yoh1 Thanking you in anticipation. On 13/04/2010 1:49 PM, Jignesh Patel wrote: > Hello, > > while I am running grompp command, I am getting following error. > > Opening library file /usr/local/gromacs/share/ gromacs/top/ff_dum.itp > Generated 837 of the 2346 non-bonded parameter combinations > --- > Program grompp, VERSION 4.0.5 > Source code file: toppush.c, line: 947 > Fatal error: > Atomtype OS not found > > Can anyone help me to solve this problem? Yep, they can point out that atom type OS is not found. Since at this stage only you know about your topology and system preparation, and more particularly why you're trying to #include "ff_dum.itp", only you can reason why. Perhaps sharing some more detail will help... Mark -- Best Wishes, Jignesh Patel Pharmacoinformatics, NIPER -- 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] OpenMM
Hi,O On 04/13/2010 04:23 PM, PACIELLO GIULIA wrote: Even if I have followed all the instructions reported for the correct installation of GPU, CUDA, OpenMM and even if my .mdp file for the simulation is written following the features supported in the release Gromacs-OpenMM, the output of the serial code running on CPU is quite different from that of the parallel code running on GPU (.gro files). That is normal. The architectures are different and the algorithms are different so you can't expect numerically identical results. The simulated ensembles should be properly generated though. Looking at the .log file I have also noticed that the energy terms 'Angle', 'Proper Dih.''Ryckaert-Bell.','LJ-14'Coulomb-14', 'LJ (SR)', 'Coulomb (SR), 'RF excl', are null for the simulation performed with the parallel code. OpenMM doesn't report individual energy and force terms, only the totals. This is done for efficiency reasons - it saves GPU memory and avoids slow CPU<->GPU transfers. Rossen -- 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] combining energy files
Hello, I am a running a simulation of 100ns, so I have two edr files md.edr and md.part0002.edr. When I calculate some of the energy values using g_energy for each of the .edr files individually I get the following result: For md.edr: Statistics over 27120401 steps [ 0. thru 54240.8008 ps ], 4 data sets All averages are over 271205 frames Energy Average RMSD Fluct. Drift Tot-Drift --- Temperature 297.9963.759733.75972 6.88223e-07 0.0373298 Pressure (bar) 1.66199262.287262.287 -2.24459e-05 -1.21748 Volume 66.16170.397280.39728 0 0 Density (SI)983.9245.902925.90292 -1.44217e-07 -0.00782243 Heat Capacity Cv: 12.4747 J/mol K (factor = 0.000159181) Isothermal Compressibility: 5.79816e-05 /bar Adiabatic bulk modulus:17246.9 bar For md.part0002.edr Statistics over 22986601 steps [ 54026.8008 thru 10.0078 ps ], 4 data sets All averages are over 229867 frames Energy Average RMSD Fluct. Drift Tot-Drift --- Temperature 297.9933.753983.75397 -5.66217e-07 -0.0260308 Pressure (bar) 1.51511263.692263.692 4.88234e-05 2.24457 Volume 66.1617 0.3984940.39849 1.29794e-07 0.00596703 Density (SI)983.924 5.93295.93284 -1.92684e-06 -0.088583 Heat Capacity Cv: 12.4747 J/mol K (factor = 0.000158697) Isothermal Compressibility: 5.8337e-05 /bar Adiabatic bulk modulus:17141.8 bar But then when I combined my .edr files using eneconv -f md.edr md.part002.edr. the output is saved into 'fixed.edr' and when I ran fixed.edr file through g_energy, I get negative values as follows : Statistics over 5001 steps [ 0. thru 10.0078 ps ], 4 data sets All averages are exact over 5001 steps Energy Average RMSD Fluct. Drift Tot-Drift --- Temperature -5.90251e-06 0 0 0 0 Pressure (bar) 4.46175e-06 0 0 -9.66961e-07 -0.0966961 Volume -1.32585e-06 0 0 0 0 Density (SI) -1.96389e-05 0 0 -2.119e-07 -0.02119 Heat Capacity Cv: 12.4718 J/mol K (factor = 0) Isothermal Compressibility: 0 /bar Adiabatic bulk modulus:inf bar I don't understand what happened there. Could someone please help me understand if I am combining the files correctly, or it is something I am missing. Thanks Nisha Patel -- 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] Question about setting deprotonated cys in enzyme structure ....
Dear all I am preparing the topology for my enzyme molecule using pdb2gmx tool. But first of all, I run a PROPKA program in order to assign the correct protonation state for my molecule. As a result of this calculation I obtained a pair of cysteines which should be deprotonated at pH 7 (fisiological pH), and others which should be protonated (the most of them). I have two questions: 1) Is it a correct aproximation to accept the protonation state obtained by these kind of methods to assign the charges of my enzyme's residues? 2) How can I manage to select which cysteines are deprotonated and which are not, using pdb2gmx tool? Any help will appreciated. -- Dr. Sergio Garay Facultad de Bioquimica y Cs. Biológicas Universidad Nacional del Litoral Santa Fe - Argentina C.C. 242 - Ciudad Universitaria - C.P. S3000ZAA Argentina Ph. +54 (342) 4575-213 Fax. +54 (342) 4575-221 -- 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] Question about setting deprotonated cys in enzyme structure ....
Alberto Sergio Garay wrote: Dear all I am preparing the topology for my enzyme molecule using pdb2gmx tool. But first of all, I run a PROPKA program in order to assign the correct protonation state for my molecule. As a result of this calculation I obtained a pair of cysteines which should be deprotonated at pH 7 (fisiological pH), and others which should be protonated (the most of them). Should they be deprotonated such that they bear a net -1 charge, or connected via disulfide bond? I have two questions: 1) Is it a correct aproximation to accept the protonation state obtained by these kind of methods to assign the charges of my enzyme's residues? I suppose that depends on the inherent approximations or limitations of the pKa calculation method. Certainly considering pKa values makes for a more accurate model than blindly assuming certain protonation states, but probably the primary literature of the calculation method(s) will describe advantages, limitations, approximations, etc. You can probably make an argument either way based on what's published. 2) How can I manage to select which cysteines are deprotonated and which are not, using pdb2gmx tool? The first consideration is whether or not you want to use a force field for which parameters have been derived for this species. As far as I know, only the AMBER force fields (by default) contain parameters for a cysteine that bears a net -1 charge. There may be parameters out there for other force fields, though. Using the AMBER force fields (after installing the ffamber ports) will require that you name the residues appropriately in the input coordinate file when running pdb2gmx. That is, your deprotonated CYS would have to be named CYM to be interpreted correctly. -Justin Any help will 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
Re: [gmx-users] combining energy files
That looks like a nice bug! You should specify which gmx version you are using. That would help getting it fixed. On Apr 13, 2010, at 21:34, nishap.pa...@utoronto.ca wrote: Hello, I am a running a simulation of 100ns, so I have two edr files md.edr and md.part0002.edr. When I calculate some of the energy values using g_energy for each of the .edr files individually I get the following result: For md.edr: Statistics over 27120401 steps [ 0. thru 54240.8008 ps ], 4 data sets All averages are over 271205 frames Energy Average RMSD Fluct. Drift Tot-Drift --- --- --- -- Temperature 297.9963.759733.75972 6.88223e-07 0.0373298 Pressure (bar) 1.66199262.287262.287 -2.24459e-05 -1.21748 Volume 66.16170.397280.39728 0 0 Density (SI)983.9245.902925.90292 -1.44217e-07 -0.00782243 Heat Capacity Cv: 12.4747 J/mol K (factor = 0.000159181) Isothermal Compressibility: 5.79816e-05 /bar Adiabatic bulk modulus:17246.9 bar For md.part0002.edr Statistics over 22986601 steps [ 54026.8008 thru 10.0078 ps ], 4 data sets All averages are over 229867 frames Energy Average RMSD Fluct. Drift Tot-Drift --- --- --- -- Temperature 297.9933.753983.75397 -5.66217e-07 -0.0260308 Pressure (bar) 1.51511263.692263.692 4.88234e-052.24457 Volume 66.1617 0.3984940.39849 1.29794e-07 0.00596703 Density (SI)983.924 5.93295.93284 -1.92684e-06 -0.088583 Heat Capacity Cv: 12.4747 J/mol K (factor = 0.000158697) Isothermal Compressibility: 5.8337e-05 /bar Adiabatic bulk modulus:17141.8 bar But then when I combined my .edr files using eneconv -f md.edr md.part002.edr. the output is saved into 'fixed.edr' and when I ran fixed.edr file through g_energy, I get negative values as follows : Statistics over 5001 steps [ 0. thru 10.0078 ps ], 4 data sets All averages are exact over 5001 steps Energy Average RMSD Fluct. Drift Tot-Drift --- --- --- -- Temperature -5.90251e-06 0 0 0 0 Pressure (bar) 4.46175e-06 0 0 -9.66961e-07 -0.0966961 Volume -1.32585e-06 0 0 0 0 Density (SI) -1.96389e-05 0 0 -2.119e-07 -0.02119 Heat Capacity Cv: 12.4718 J/mol K (factor = 0) Isothermal Compressibility: 0 /bar Adiabatic bulk modulus:inf bar I don't understand what happened there. Could someone please help me understand if I am combining the files correctly, or it is something I am missing. Thanks Nisha Patel -- 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] Question about setting deprotonated cys in enzyme structure ....
On Apr 13, 2010, at 21:23, Alberto Sergio Garay wrote: Dear all I am preparing the topology for my enzyme molecule using pdb2gmx tool. But first of all, I run a PROPKA program in order to assign the correct protonation state for my molecule. As a result of this calculation I obtained a pair of cysteines which should be deprotonated at pH 7 (fisiological pH), and others which should be protonated (the most of them). I have two questions: 1) Is it a correct aproximation to accept the protonation state obtained by these kind of methods to assign the charges of my enzyme's residues? Depends a lot in how the method is doing it. I never heard of that one, which does not mean it is bad :)) However diprotonated cysteine at pH 7 is a bit weard! Could it be you have a di-sulfide bridge? 2) How can I manage to select which cysteines are deprotonated and which are not, using pdb2gmx tool? You can get them bridged but not deprotonated. Option -cys IIRC. Any help will appreciated. -- Dr. Sergio Garay Facultad de Bioquimica y Cs. Biológicas Universidad Nacional del Litoral Santa Fe - Argentina C.C. 242 - Ciudad Universitaria - C.P. S3000ZAA Argentina Ph. +54 (342) 4575-213 Fax. +54 (342) 4575-221 -- 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] combining energy files
I am using gromacs-4.0.5. Thanks. Quoting XAvier Periole : That looks like a nice bug! You should specify which gmx version you are using. That would help getting it fixed. On Apr 13, 2010, at 21:34, nishap.pa...@utoronto.ca wrote: Hello, I am a running a simulation of 100ns, so I have two edr files md.edr and md.part0002.edr. When I calculate some of the energy values using g_energy for each of the .edr files individually I get the following result: For md.edr: Statistics over 27120401 steps [ 0. thru 54240.8008 ps ], 4 data sets All averages are over 271205 frames Energy Average RMSD Fluct. Drift Tot-Drift --- Temperature 297.9963.759733.75972 6.88223e-07 0.0373298 Pressure (bar) 1.66199262.287262.287 -2.24459e-05 -1.21748 Volume 66.16170.397280.39728 0 0 Density (SI)983.9245.902925.90292 -1.44217e-07 -0.00782243 Heat Capacity Cv: 12.4747 J/mol K (factor = 0.000159181) Isothermal Compressibility: 5.79816e-05 /bar Adiabatic bulk modulus:17246.9 bar For md.part0002.edr Statistics over 22986601 steps [ 54026.8008 thru 10.0078 ps ], 4 data sets All averages are over 229867 frames Energy Average RMSD Fluct. Drift Tot-Drift --- Temperature 297.9933.753983.75397 -5.66217e-07 -0.0260308 Pressure (bar) 1.51511263.692263.692 4.88234e-05 2.24457 Volume 66.1617 0.3984940.39849 1.29794e-07 0.00596703 Density (SI)983.924 5.93295.93284 -1.92684e-06 -0.088583 Heat Capacity Cv: 12.4747 J/mol K (factor = 0.000158697) Isothermal Compressibility: 5.8337e-05 /bar Adiabatic bulk modulus:17141.8 bar But then when I combined my .edr files using eneconv -f md.edr md.part002.edr. the output is saved into 'fixed.edr' and when I ran fixed.edr file through g_energy, I get negative values as follows : Statistics over 5001 steps [ 0. thru 10.0078 ps ], 4 data sets All averages are exact over 5001 steps Energy Average RMSD Fluct. Drift Tot-Drift --- Temperature -5.90251e-06 0 0 0 0 Pressure (bar) 4.46175e-06 0 0 -9.66961e-07 -0.0966961 Volume -1.32585e-06 0 0 0 0 Density (SI) -1.96389e-05 0 0 -2.119e-07 -0.02119 Heat Capacity Cv: 12.4718 J/mol K (factor = 0) Isothermal Compressibility: 0 /bar Adiabatic bulk modulus:inf bar I don't understand what happened there. Could someone please help me understand if I am combining the files correctly, or it is something I am missing. Thanks Nisha Patel -- 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 thewww 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] combining energy files
nishap.pa...@utoronto.ca wrote: I am using gromacs-4.0.5. Try upgrading to the newest version (4.0.7), and if that does not fix the problem, please report back with the exact command line, gmxcheck output (on the .edr file), compilers used, hardware, etc. -Justin Thanks. Quoting XAvier Periole : That looks like a nice bug! You should specify which gmx version you are using. That would help getting it fixed. On Apr 13, 2010, at 21:34, nishap.pa...@utoronto.ca wrote: Hello, I am a running a simulation of 100ns, so I have two edr files md.edr and md.part0002.edr. When I calculate some of the energy values using g_energy for each of the .edr files individually I get the following result: For md.edr: Statistics over 27120401 steps [ 0. thru 54240.8008 ps ], 4 data sets All averages are over 271205 frames Energy Average RMSD Fluct. Drift Tot-Drift --- Temperature 297.9963.759733.75972 6.88223e-07 0.0373298 Pressure (bar) 1.66199262.287262.287 -2.24459e-05 -1.21748 Volume 66.16170.397280.39728 0 0 Density (SI)983.9245.902925.90292 -1.44217e-07 -0.00782243 Heat Capacity Cv: 12.4747 J/mol K (factor = 0.000159181) Isothermal Compressibility: 5.79816e-05 /bar Adiabatic bulk modulus:17246.9 bar For md.part0002.edr Statistics over 22986601 steps [ 54026.8008 thru 10.0078 ps ], 4 data sets All averages are over 229867 frames Energy Average RMSD Fluct. Drift Tot-Drift --- Temperature 297.9933.753983.75397 -5.66217e-07 -0.0260308 Pressure (bar) 1.51511263.692263.692 4.88234e-05 2.24457 Volume 66.1617 0.3984940.39849 1.29794e-07 0.00596703 Density (SI)983.924 5.93295.93284 -1.92684e-06 -0.088583 Heat Capacity Cv: 12.4747 J/mol K (factor = 0.000158697) Isothermal Compressibility: 5.8337e-05 /bar Adiabatic bulk modulus:17141.8 bar But then when I combined my .edr files using eneconv -f md.edr md.part002.edr. the output is saved into 'fixed.edr' and when I ran fixed.edr file through g_energy, I get negative values as follows : Statistics over 5001 steps [ 0. thru 10.0078 ps ], 4 data sets All averages are exact over 5001 steps Energy Average RMSD Fluct. Drift Tot-Drift --- Temperature -5.90251e-06 0 0 0 0 Pressure (bar) 4.46175e-06 0 0 -9.66961e-07 -0.0966961 Volume -1.32585e-06 0 0 0 0 Density (SI) -1.96389e-05 0 0 -2.119e-07 -0.02119 Heat Capacity Cv: 12.4718 J/mol K (factor = 0) Isothermal Compressibility: 0 /bar Adiabatic bulk modulus:inf bar I don't understand what happened there. Could someone please help me understand if I am combining the files correctly, or it is something I am missing. Thanks Nisha Patel -- 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 thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: How to prepare the two tolopogy files when doing TI calculation?
Dear Mark, I know that the tutorial can go through, my problem is just how to generate the two topology files. From the tutorial, I know how to run TI calculation, but first, I got to know how to prepare these files, both for topology and coordinate files. I will highly appreciate for your suggestion if you can help me! Thanks! All the best, Qinghua > Date: Wed, 14 Apr 2010 00:09:16 +1000 > From: Mark Abraham > Subject: Re: [gmx-users] How to prepare the two tolopogy files when > doing TI calculation? > To: Discussion list for GROMACS users > Message-ID: <4bc47b0c.4020...@anu.edu.au> > Content-Type: text/plain; charset=x-gbk; format=flowed > > On 13/04/2010 7:35 PM, fancy2012 wrote: > > Dear GMX users, > > I want to do some TI calculation using GMX, and I have learned the > > tutorial of TI calculation from this web site > > http://www.dillgroup.ucsf.edu/group/wiki/index.php/Free_Energy:_Tutorial. > > So I have know how to run TI calculations. But there is still a problem. > > I don't know how to prepare the two topology files, which are initial > > and final states, respectively. Could somebody give me some suggestion > > on it? Any response will be highly appreciated! Thanks! > > Didn't the tutorial go through that? Look at its examples. > > 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] Re: How to prepare the two tolopogy files when doing TI calculation?
fancy2012 wrote: Dear Mark, I know that the tutorial can go through, my problem is just how to generate the two topology files. From the tutorial, I know how to run TI calculation, but first, I got to know how to prepare these files, both for topology and coordinate files. I will highly appreciate for your suggestion if you can help me! Thanks! Be advised that calculating free energies in Gromacs-4.0.x is different from the instructions in the tutorial, which are for version 3.3.x; topology manipulation is no longer necessary and the methods for decoupling are controlled by settings in the .mdp file. You haven't said which version of Gromacs you're using, but that is quite important. There are several threads in the list archive that discuss free energy calculations in Gromacs-4.0.x. There are no tutorials, however. There are various programs in the User Contribution section of the Gromacs site for generating small molecule topologies, as well as the PRODRG server for Gromos topologies. The parameters that any of these programs give are not necessarily 100% reliable (especially in the case of PRODRG). Generating a coordinate file is going to depend on what you're doing. If you have a simple small molecule in water, you'll have to have some initial configuration for the solute and there are many tools that can be used for that purpose. Solvent can be added with genbox. But since you haven't given any details of what it is that you're trying to accomplish, that's about as precise as any advice can get. -Justin All the best, Qinghua Date: Wed, 14 Apr 2010 00:09:16 +1000 From: Mark Abraham Subject: Re: [gmx-users] How to prepare the two tolopogy files when doing TI calculation? To: Discussion list for GROMACS users Message-ID: <4bc47b0c.4020...@anu.edu.au> Content-Type: text/plain; charset=x-gbk; format=flowed On 13/04/2010 7:35 PM, fancy2012 wrote: > Dear GMX users, > I want to do some TI calculation using GMX, and I have learned the > tutorial of TI calculation from this web site > http://www.dillgroup.ucsf.edu/group/wiki/index.php/Free_Energy:_Tutorial. > So I have know how to run TI calculations. But there is still a problem. > I don't know how to prepare the two topology files, which are initial > and final states, respectively. Could somebody give me some suggestion > on it? Any response will be highly appreciated! Thanks! Didn't the tutorial go through that? Look at its examples. Mark -- 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] questions about energy minimization
To whom may be concerned, I am just doing an energy minimization on a polymer chain ---PVA, which contains 50 repeat units. I am puzzled about how to choose an appropriate emtol. It's said to be a maximum force in the system. But how to make sure that the emtol I choose is big or small enough that my system will finally well equilibrium? After I finished the energy minimization, when the maximum force is actually under the emmtol, I compare the potential to a previou energy minimization work using some other software like Material Studio, It is the finally potential that surprise me a lot. The potential I get using gromacs is still positive and with a magnitude of e~03 whist using Material Studio it is negative and with the same magnitude.Why so? Is there any reference I can refer to? Thanks in advanced. celeste 2010-04-14 -- 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] questions about energy minimization
On 14/04/2010 1:28 PM, DreamCatcher wrote: To whom may be concerned, I am just doing an energy minimization on a polymer chain ---PVA, which contains 50 repeat units. I am puzzled about how to choose an appropriate emtol. It's said to be a maximum force in the system. But how to make sure that the emtol I choose is big or small enough that my system will finally well equilibrium? That depends on the purpose to which you intend to put it. For preparation for MD, so long as the subsequent equilibration process doesn't explode, you minimized enough. After I finished the energy minimization, when the maximum force is actually under the emmtol, I compare the potential to a previou energy minimization work using some other software like Material Studio, It is the finally potential that surprise me a lot. The potential I get using gromacs is still positive and with a magnitude of e~03 whist using Material Studio it is negative and with the same magnitude.Why so? Is there any reference I can refer to? That will mean you have something nonphysical in your structure file (e.g. overlapping atoms) or model physics (broken parameters or file formats). In such cases EM may or may not help. 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] OpenMM
Hi, thanks a lot for your answer, but I have some doubts yet... My .gro files are very different and I'm not sure that the architecture (CPU / GPU) could influence the result so much as in my example (the first is the output of the serial code and the second that of the parallel ones). SERIAL CODE: 1LYSH N1 3.240 2.123 0.830 0.0828 0.7601 -0.2788 1LYSHCA2 3.114 2.170 0.777 -0.1210 0.1179 -0.3660 1LYSHCB3 3.060 2.258 0.889 -0.1060 0.0142 -0.2772 1LYSHCG4 3.103 2.403 0.867 -1.1970 0.3922 0.0170 1LYSHCD5 3.078 2.498 0.983 -0.5172 1.0015 -0.3267 1LYSHCE6 3.120 2.451 1.122 -0.5706 0.5624 -0.4567 1LYSHNZ7 3.024 2.505 1.220 0.2425 1.4466 -0.1367 1LYSH C8 3.006 2.065 0.754 0.1697 -0.4396 0.7191 1LYSH O9 2.896 2.086 0.701 0.0216 -1.3952 0.6269 2VAL N 10 3.036 1.943 0.799 0.5429 -0.4260 0.5099 2VAL H 11 3.132 1.933 0.831 0.8289 0.8067 0.0933 2VAL CA 12 2.955 1.826 0.822 0.2219 -0.3946 -0.4277 PARALLEL CODE: 1LYSH N1 3.333 1.969 0.702 -0.4164 -0.1749 -0.1669 1LYSHCA2 3.221 2.054 0.737 -0.0727 0.2241 -0.0385 1LYSHCB3 3.163 2.122 0.613 -0.1387 -0.2965 -0.2935 1LYSHCG4 3.219 2.261 0.586 0.0989 -0.2444 0.4520 1LYSHCD5 3.100 2.352 0.558 0.5215 0.0874 -0.3041 1LYSHCE6 3.123 2.486 0.627 -0.1705 0.3629 -0.6025 1LYSHNZ7 2.996 2.514 0.696 -0.2146 0.6887 -0.8084 1LYSH C8 3.110 1.973 0.800 -0.1975 -0.0906 -0.6520 1LYSH O9 3.007 2.030 0.837 0.2640 0.4243 -0.1313 2VAL N 10 3.141 1.849 0.840 0.2749 -0.0187 -0.7992 2VAL H 11 3.238 1.824 0.826 0.5334 0.1303 0.6497 2VAL CA 12 3.050 1.754 0.901 0.8255 0.0012 0.0684 Then, even if in the .log file (parallel code), the energy terms are null at every time step to avoid slow communication between GPU and CPU, the average energies are null too. (I have test this also using g_energy) AVERAGES: Energies (kJ/mol) AngleProper Dih. Ryckaert-Bell. LJ-14 Coulomb-14 0.0e+000.0e+000.0e+00 0.0e+000.0e+00 LJ (SR) Coulomb (SR) RF excl. PotentialKinetic En. 0.0e+000.0e+000.0e+00 -1.05419e+065.24361e+05 Total EnergyTemperature Pressure (bar) Cons. rmsd () -5.29827e+053.39337e+040.0e+00 0.0e+00 Thanks in advance, Giulia On Tue, 13 Apr 2010 19:14:29 +0200 Rossen Apostolov wrote: Hi,O On 04/13/2010 04:23 PM, PACIELLO GIULIA wrote: Even if I have followed all the instructions reported for the correct installation of GPU, CUDA, OpenMM and even if my .mdp file for the simulation is written following the features supported in the release Gromacs-OpenMM, the output of the serial code running on CPU is quite different from that of the parallel code running on GPU (.gro files). That is normal. The architectures are different and the algorithms are different so you can't expect numerically identical results. The simulated ensembles should be properly generated though. Looking at the .log file I have also noticed that the energy terms 'Angle', 'Proper Dih.''Ryckaert-Bell.','LJ-14'Coulomb-14', 'LJ (SR)', 'Coulomb (SR), 'RF excl', are null for the simulation performed with the parallel code. OpenMM doesn't report individual energy and force terms, only the totals. This is done for efficiency reasons - it saves GPU memory and avoids slow CPU<->GPU transfers. Rossen -- 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] OpenMM
On 14/04/2010 4:31 PM, PACIELLO GIULIA wrote: Hi, thanks a lot for your answer, but I have some doubts yet... My .gro files are very different and I'm not sure that the architecture (CPU / GPU) could influence the result so much as in my example (the first is the output of the serial code and the second that of the parallel ones). MD is chaotic. Tiny differences at an early stage lead to wildly different results later. That's inevitable. However ensemble averages should converge to the same value. SERIAL CODE: 1LYSH N 1 3.240 2.123 0.830 0.0828 0.7601 -0.2788 1LYSH CA 2 3.114 2.170 0.777 -0.1210 0.1179 -0.3660 1LYSH CB 3 3.060 2.258 0.889 -0.1060 0.0142 -0.2772 1LYSH CG 4 3.103 2.403 0.867 -1.1970 0.3922 0.0170 1LYSH CD 5 3.078 2.498 0.983 -0.5172 1.0015 -0.3267 1LYSH CE 6 3.120 2.451 1.122 -0.5706 0.5624 -0.4567 1LYSH NZ 7 3.024 2.505 1.220 0.2425 1.4466 -0.1367 1LYSH C 8 3.006 2.065 0.754 0.1697 -0.4396 0.7191 1LYSH O 9 2.896 2.086 0.701 0.0216 -1.3952 0.6269 2VAL N 10 3.036 1.943 0.799 0.5429 -0.4260 0.5099 2VAL H 11 3.132 1.933 0.831 0.8289 0.8067 0.0933 2VAL CA 12 2.955 1.826 0.822 0.2219 -0.3946 -0.4277 PARALLEL CODE: 1LYSH N 1 3.333 1.969 0.702 -0.4164 -0.1749 -0.1669 1LYSH CA 2 3.221 2.054 0.737 -0.0727 0.2241 -0.0385 1LYSH CB 3 3.163 2.122 0.613 -0.1387 -0.2965 -0.2935 1LYSH CG 4 3.219 2.261 0.586 0.0989 -0.2444 0.4520 1LYSH CD 5 3.100 2.352 0.558 0.5215 0.0874 -0.3041 1LYSH CE 6 3.123 2.486 0.627 -0.1705 0.3629 -0.6025 1LYSH NZ 7 2.996 2.514 0.696 -0.2146 0.6887 -0.8084 1LYSH C 8 3.110 1.973 0.800 -0.1975 -0.0906 -0.6520 1LYSH O 9 3.007 2.030 0.837 0.2640 0.4243 -0.1313 2VAL N 10 3.141 1.849 0.840 0.2749 -0.0187 -0.7992 2VAL H 11 3.238 1.824 0.826 0.5334 0.1303 0.6497 2VAL CA 12 3.050 1.754 0.901 0.8255 0.0012 0.0684 Then, even if in the .log file (parallel code), the energy terms are null at every time step to avoid slow communication between GPU and CPU, the average energies are null too. (I have test this also using g_energy) AVERAGES: Energies (kJ/mol) Angle Proper Dih. Ryckaert-Bell. LJ-14 Coulomb-14 0.0e+00 0.0e+00 0.0e+00 0.0e+00 0.0e+00 LJ (SR) Coulomb (SR) RF excl. Potential Kinetic En. 0.0e+00 0.0e+00 0.0e+00 -1.05419e+06 5.24361e+05 Total Energy Temperature Pressure (bar) Cons. rmsd () -5.29827e+05 3.39337e+04 0.0e+00 0.0e+00 There's no evidence of a problem here, given that because the GPU version will not report such energies, there's nothing to average. 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] OpenMM
Ok...so how could I know the energies among atoms? And how can I test if my parallel code is running in the correct manner? Thanks, Giulia On Wed, 14 Apr 2010 16:43:13 +1000 Mark Abraham wrote: On 14/04/2010 4:31 PM, PACIELLO GIULIA wrote: Hi, thanks a lot for your answer, but I have some doubts yet... My .gro files are very different and I'm not sure that the architecture (CPU / GPU) could influence the result so much as in my example (the first is the output of the serial code and the second that of the parallel ones). MD is chaotic. Tiny differences at an early stage lead to wildly different results later. That's inevitable. However ensemble averages should converge to the same value. SERIAL CODE: 1LYSH N 1 3.240 2.123 0.830 0.0828 0.7601 -0.2788 1LYSH CA 2 3.114 2.170 0.777 -0.1210 0.1179 -0.3660 1LYSH CB 3 3.060 2.258 0.889 -0.1060 0.0142 -0.2772 1LYSH CG 4 3.103 2.403 0.867 -1.1970 0.3922 0.0170 1LYSH CD 5 3.078 2.498 0.983 -0.5172 1.0015 -0.3267 1LYSH CE 6 3.120 2.451 1.122 -0.5706 0.5624 -0.4567 1LYSH NZ 7 3.024 2.505 1.220 0.2425 1.4466 -0.1367 1LYSH C 8 3.006 2.065 0.754 0.1697 -0.4396 0.7191 1LYSH O 9 2.896 2.086 0.701 0.0216 -1.3952 0.6269 2VAL N 10 3.036 1.943 0.799 0.5429 -0.4260 0.5099 2VAL H 11 3.132 1.933 0.831 0.8289 0.8067 0.0933 2VAL CA 12 2.955 1.826 0.822 0.2219 -0.3946 -0.4277 PARALLEL CODE: 1LYSH N 1 3.333 1.969 0.702 -0.4164 -0.1749 -0.1669 1LYSH CA 2 3.221 2.054 0.737 -0.0727 0.2241 -0.0385 1LYSH CB 3 3.163 2.122 0.613 -0.1387 -0.2965 -0.2935 1LYSH CG 4 3.219 2.261 0.586 0.0989 -0.2444 0.4520 1LYSH CD 5 3.100 2.352 0.558 0.5215 0.0874 -0.3041 1LYSH CE 6 3.123 2.486 0.627 -0.1705 0.3629 -0.6025 1LYSH NZ 7 2.996 2.514 0.696 -0.2146 0.6887 -0.8084 1LYSH C 8 3.110 1.973 0.800 -0.1975 -0.0906 -0.6520 1LYSH O 9 3.007 2.030 0.837 0.2640 0.4243 -0.1313 2VAL N 10 3.141 1.849 0.840 0.2749 -0.0187 -0.7992 2VAL H 11 3.238 1.824 0.826 0.5334 0.1303 0.6497 2VAL CA 12 3.050 1.754 0.901 0.8255 0.0012 0.0684 Then, even if in the .log file (parallel code), the energy terms are null at every time step to avoid slow communication between GPU and CPU, the average energies are null too. (I have test this also using g_energy) AVERAGES: Energies (kJ/mol) Angle Proper Dih. Ryckaert-Bell. LJ-14 Coulomb-14 0.0e+00 0.0e+00 0.0e+00 0.0e+00 0.0e+00 LJ (SR) Coulomb (SR) RF excl. Potential Kinetic En. 0.0e+00 0.0e+00 0.0e+00 -1.05419e+06 5.24361e+05 Total Energy Temperature Pressure (bar) Cons. rmsd () -5.29827e+05 3.39337e+04 0.0e+00 0.0e+00 There's no evidence of a problem here, given that because the GPU version will not report such energies, there's nothing to average. 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
Re: [gmx-users] OpenMM
On 14/04/2010 4:52 PM, PACIELLO GIULIA wrote: Ok...so how could I know the energies among atoms? Since it's not reported, you can't get breakdowns of energies. That's a limitation from the use of GPU. If you want this information, perhaps do your simulation on the GPU and re-rerun selected frames from your trajectory on a different machine that does not use GPUs. And how can I test if my parallel code is running in the correct manner? MD is chaotic. Tiny differences at an early stage lead to wildly different results later. That's inevitable. However ensemble averages should converge to the same value. Do things converge to the same values? There's a chance that mdrun -reprod will lead to equivalent total energies after only one step, if that's been implemented that way. 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
