[gmx-users] flexiable water - model
Hello, I am trying to run a simulation for flexiable water. I use the parameters from J. Chem. Phys. (2006),124,024503 paper and made floowing changes. I addes WAT as a new residue name in aminoacids.dat I addred two atom times in ffoplsaa.atp opls_1001 15.99940 ; O SPC_fw Water opls_10021.00800 ; H SPC_fw Water I added following parameters in ffoplsaa.rtp [ WAT] [ atoms ] OWA opls_1001 -0.82 1 HWA1 opls_1002 0.41 2 HWA2 opls_1002 0.41 2 [ bonds ] OWA HWA1 OWA HWA2 I made a spc_fw.itp file. ; Derived from parsing of runfiles/alat.top.orig [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ ;1 3 yes 0.5 0.5 ; comb-rule 3 is square-root sigma, the OPLSAA version [ atomtypes ] ; full atom descriptions are available in ffoplsaa.atp ; name bond_typemasscharge ptype sigma epsilon opls_1001 OWA 815.99940 -0.820 A3.1655e-01 6.503e-01 opls_1002 HWA 1 1.00800 0.410 A0.00e+00 0.00e+00 [ bondtypes ] ; ij func b0 kb OWAHWA 10.1012 443153.3808 ; J. Chem. Phys. (2006),124,024503 [ angletypes ] ; ijk func th0 cth HWA OWA HWA 1 113.24 317.5656 ; J. Chem. Phys. (2006),124,024503 [ moleculetype ] ; Namenrexcl WAT 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 1 opls_1001 1WAT OWA 1 -0.82 2 opls_1002 1WATHWA1 1 0.41 3 opls_1002 1WATHWA2 1 0.41 [ bonds ] ; i j funct 1 2 1 1 3 1 [ angles ] ; i j k funct 2 1 3 1 Finally I made changes in ffoplsaa.itp file ;#include ffoplsaanb.itp ;#include ffoplsaabon.itp #include spc_fw.itp #include spc_fw_mol.itp For pdb2gmx pdb2gmx -f water.pdb -o water.pdb -p water.top -ter I get following error Fatal error: Atom OWA in residue HOH 1 not found in rtp entry with 3 atoms while sorting atoms WHy is reading HOH residue. In my pdb file I mentioned WAT as residure. How can I fix this error? 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/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] reg pulling of o2 towards fe atom
Dear gmx user, i wanted to simulate cooperativity effect of heamoglobin through steered MD for that i need to pull oxygen molecule at the same time Fe atom of phorphyrin ring (protruding above the plane of Phorphyrin ring in the initial PDB) should go to the plane of phorphyrin ring (that is movement of both Fe and oxygen with different rate ) without any reference group for pulling Is it possible in gromacs? thanks in advance -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] flexiable water - model
Nilesh Dhumal wrote: Hello, I am trying to run a simulation for flexiable water. I use the parameters from J. Chem. Phys. (2006),124,024503 paper and made floowing changes. I addes WAT as a new residue name in aminoacids.dat I addred two atom times in ffoplsaa.atp opls_1001 15.99940 ; O SPC_fw Water opls_10021.00800 ; H SPC_fw Water I added following parameters in ffoplsaa.rtp [ WAT] [ atoms ] OWA opls_1001 -0.82 1 HWA1 opls_1002 0.41 2 HWA2 opls_1002 0.41 2 [ bonds ] OWA HWA1 OWA HWA2 I made a spc_fw.itp file. ; Derived from parsing of runfiles/alat.top.orig [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ ;1 3 yes 0.5 0.5 ; comb-rule 3 is square-root sigma, the OPLSAA version [ atomtypes ] ; full atom descriptions are available in ffoplsaa.atp ; name bond_typemasscharge ptype sigma epsilon opls_1001 OWA 815.99940 -0.820 A3.1655e-01 6.503e-01 opls_1002 HWA 1 1.00800 0.410 A0.00e+00 0.00e+00 [ bondtypes ] ; ij func b0 kb OWAHWA 10.1012 443153.3808 ; J. Chem. Phys. (2006),124,024503 [ angletypes ] ; ijk func th0 cth HWA OWA HWA 1 113.24 317.5656 ; J. Chem. Phys. (2006),124,024503 [ moleculetype ] ; Namenrexcl WAT 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 1 opls_1001 1WAT OWA 1 -0.82 2 opls_1002 1WATHWA1 1 0.41 3 opls_1002 1WATHWA2 1 0.41 [ bonds ] ; i j funct 1 2 1 1 3 1 [ angles ] ; i j k funct 2 1 3 1 Finally I made changes in ffoplsaa.itp file ;#include ffoplsaanb.itp ;#include ffoplsaabon.itp #include spc_fw.itp #include spc_fw_mol.itp For pdb2gmx pdb2gmx -f water.pdb -o water.pdb -p water.top -ter I get following error Fatal error: Atom OWA in residue HOH 1 not found in rtp entry with 3 atoms while sorting atoms WHy is reading HOH residue. In my pdb file I mentioned WAT as residure. How can I fix this error? If I recall, pdb2gmx does some internal translations to standardize water nomenclature. In reality, you don't need pdb2gmx at all - you've already shown that you're created a topology for the water model. -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/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] flexiable water - model
I have total 256 water molecules. I am trying to genrate the .top file from .pdb so I used pdb2gmx. How can I genrate the .top file with pdb2gmx for 256 water molecules. Nilesh On Tue, April 26, 2011 1:01 pm, Justin A. Lemkul wrote: Nilesh Dhumal wrote: Hello, I am trying to run a simulation for flexiable water. I use the parameters from J. Chem. Phys. (2006),124,024503 paper and made floowing changes. I addes WAT as a new residue name in aminoacids.dat I addred two atom times in ffoplsaa.atp opls_1001 15.99940 ; O SPC_fw Water opls_10021.00800 ; H SPC_fw Water I added following parameters in ffoplsaa.rtp [ WAT] [ atoms ] OWA opls_1001 -0.82 1 HWA1 opls_1002 0.41 2 HWA2 opls_1002 0.41 2 [ bonds ] OWA HWA1 OWA HWA2 I made a spc_fw.itp file. ; Derived from parsing of runfiles/alat.top.orig [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ ;1 3 yes 0.5 0.5 ; comb-rule 3 is square-root sigma, the OPLSAA version [ atomtypes ] ; full atom descriptions are available in ffoplsaa.atp ; name bond_typemasscharge ptype sigma epsilon opls_1001 OWA 815.99940 -0.820 A3.1655e-01 6.503e-01 opls_1002 HWA 1 1.00800 0.410 A0.00e+00 0.00e+00 [ bondtypes ] ; ij func b0 kb OWAHWA 10.1012 443153.3808 ; J. Chem. Phys. (2006),124,024503 [ angletypes ] ; ijk func th0 cth HWA OWA HWA 1 113.24 317.5656 ; J. Chem. Phys. (2006),124,024503 [ moleculetype ] ; Namenrexcl WAT 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 1 opls_1001 1WAT OWA 1 -0.82 2 opls_1002 1WATHWA1 1 0.41 3 opls_1002 1WATHWA2 1 0.41 [ bonds ] ; i j funct 1 2 1 1 3 1 [ angles ] ; i j k funct 2 1 3 1 Finally I made changes in ffoplsaa.itp file ;#include ffoplsaanb.itp ;#include ffoplsaabon.itp #include spc_fw.itp #include spc_fw_mol.itp For pdb2gmx pdb2gmx -f water.pdb -o water.pdb -p water.top -ter I get following error Fatal error: Atom OWA in residue HOH 1 not found in rtp entry with 3 atoms while sorting atoms WHy is reading HOH residue. In my pdb file I mentioned WAT as residure. How can I fix this error? If I recall, pdb2gmx does some internal translations to standardize water nomenclature. In reality, you don't need pdb2gmx at all - you've already shown that you're created a topology for the water model. -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/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] flexiable water - model
Nilesh Dhumal wrote: I have total 256 water molecules. I am trying to genrate the .top file from .pdb so I used pdb2gmx. pdb2gmx is only really useful for building topologies for linear molecules built from repeat building blocks, not for systems of individual molecules. How can I genrate the .top file with pdb2gmx for 256 water molecules. With a text editor: #include ffoplsaa.itp #include spc_fw.itp [ system ] water [ molecules ] WAT 256 -Justin Nilesh On Tue, April 26, 2011 1:01 pm, Justin A. Lemkul wrote: Nilesh Dhumal wrote: Hello, I am trying to run a simulation for flexiable water. I use the parameters from J. Chem. Phys. (2006),124,024503 paper and made floowing changes. I addes WAT as a new residue name in aminoacids.dat I addred two atom times in ffoplsaa.atp opls_1001 15.99940 ; O SPC_fw Water opls_10021.00800 ; H SPC_fw Water I added following parameters in ffoplsaa.rtp [ WAT] [ atoms ] OWA opls_1001 -0.82 1 HWA1 opls_1002 0.41 2 HWA2 opls_1002 0.41 2 [ bonds ] OWA HWA1 OWA HWA2 I made a spc_fw.itp file. ; Derived from parsing of runfiles/alat.top.orig [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ ;1 3 yes 0.5 0.5 ; comb-rule 3 is square-root sigma, the OPLSAA version [ atomtypes ] ; full atom descriptions are available in ffoplsaa.atp ; name bond_typemasscharge ptype sigma epsilon opls_1001 OWA 815.99940 -0.820 A3.1655e-01 6.503e-01 opls_1002 HWA 1 1.00800 0.410 A0.00e+00 0.00e+00 [ bondtypes ] ; ij func b0 kb OWAHWA 10.1012 443153.3808 ; J. Chem. Phys. (2006),124,024503 [ angletypes ] ; ijk func th0 cth HWA OWA HWA 1 113.24 317.5656 ; J. Chem. Phys. (2006),124,024503 [ moleculetype ] ; Namenrexcl WAT 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 1 opls_1001 1WAT OWA 1 -0.82 2 opls_1002 1WATHWA1 1 0.41 3 opls_1002 1WATHWA2 1 0.41 [ bonds ] ; i j funct 1 2 1 1 3 1 [ angles ] ; i j k funct 2 1 3 1 Finally I made changes in ffoplsaa.itp file ;#include ffoplsaanb.itp ;#include ffoplsaabon.itp #include spc_fw.itp #include spc_fw_mol.itp For pdb2gmx pdb2gmx -f water.pdb -o water.pdb -p water.top -ter I get following error Fatal error: Atom OWA in residue HOH 1 not found in rtp entry with 3 atoms while sorting atoms WHy is reading HOH residue. In my pdb file I mentioned WAT as residure. How can I fix this error? If I recall, pdb2gmx does some internal translations to standardize water nomenclature. In reality, you don't need pdb2gmx at all - you've already shown that you're created a topology for the water model. -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/Support/Mailing_Lists/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/Support/Mailing_Lists -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] BUG in angular removal part??
Hi, gromacs developers,
It seems that there is a bug regarding the angular moment removal.
This may not be very important for many users since most of them are
doing PBC where it is irrelevant, but if you are doing cluster or if you
really care the angular momentum like I
do(I want the angular momentum to be exactly zero since this corresponds
to some quantum resolved state), then it is important.
The angular momentum removal part in mdlib/vcm.c where it evaluate
moment of inertia is wrong, subroutine *update_tensor.
*Specifically, the diagonal part is not calculated right.
According to either */Classical Mechancs, by Goldstein or Theoretical
Mechanics of Particles and Continua, by A.L.Fetter and J.D.Walecka.
I_{xx}=\sum_{i} m_{i}*(r_{i}^2-x_{i}^2), where x can be x,y,z.
But the /**update_tensor gives
**/I_{xx}=\sum_{i} m_{i}*(x_{i}^2).
/*/I initially thought there could be some other routine to
correct update_tensor, but apparently, it is calculated according to
that, and I manually calculated them and turns out my theory is right,
the update_tensor is wrong as it stands.
/Again, this would not affect, say, 99.999% of the user, but it
will always be good to have a clean code.
Thanks
/
/Xiaohu/
/
--
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[gmx-users] Placing anion/cation at a particular distance from peptide
Dear gmx users, I need to design a starting configuration of a polypeptide with charged side chains sitting in a box of water with Cl- ions within 7 ang of its radius. I realize that in such a system like charges will essentially prefer to be as far as possible from each other, but I still need the above stated configuration. Is there an easy way to specify the distance of the anions to be added from the peptide ? Thanks, SN -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] error when running grompp
Dear Gromacs users I ahve a dppc monolayer on water layer 9tip4p-2005). I have added 8 Mg and 16 Cl ions using genion and now want to use grompp and then start the simulation to see the effect of ions on the pressure-area isotherm of the system. running grompp in gromacs 3.3 I see he following error: please help em to solve it.let me knoe please what is cpp? Thanks in advance D. Aghaie -bash-3.2$ grompp_mpi -c dppc-salt-Mg-0.1.gro -f run.mdp -n indexsalt-Mg.ndx -p topoldppc.top -o topol.tpr -np 8 :-) G R O M A C S (-: Groningen Machine for Chemical Simulation :-) VERSION 3.3 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2004, The GROMACS development team, check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) grompp_mpi (-: Option Filename Type Description -f run.mdp Input, Opt! grompp input file with MD parameters -po mdout.mdp Output grompp input file with MD parameters -c dppc-salt-Mg-0.1.gro Input Generic structure: gro g96 pdb tpr tpb tpa xml -r conf.gro Input, Opt. Generic structure: gro g96 pdb tpr tpb tpa xml -rb conf.gro Input, Opt. Generic structure: gro g96 pdb tpr tpb tpa xml -n indexsalt-Mg.ndx Input, Opt! Index file -deshuf deshuf.ndx Output, Opt. Index file -p topoldppc.top Input Topology file -pp processed.top Output, Opt. Topology file -o topol.tpr Output Generic run input: tpr tpb tpa xml -t traj.trr Input, Opt. Full precision trajectory: trr trj -e ener.edr Input, Opt. Generic energy: edr ene Option Type Value Description -- -[no]h bool no Print help info and quit -[no]X bool no Use dialog box GUI to edit command line options -nice int 0 Set the nicelevel -[no]v bool yes Be loud and noisy -time real -1 Take frame at or first after this time. -np int 8 Generate statusfile for # nodes -[no]shuffle bool no Shuffle molecules over nodes -[no]sort bool no Sort molecules according to X coordinate -[no]rmvsbds bool yes Remove constant bonded interactions with virtual sites -load string Releative load capacity of each node on a parallel machine. Be sure to use quotes around the string, which should contain a number for each node -maxwarn int 10 Number of warnings after which input processing stops -[no]check14 bool no Remove 1-4 interactions without Van der Waals -[no]renum bool yes Renumber atomtypes and minimize number of atomtypes creating statusfile for 8 nodes... Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1# checking input for internal consistency... calling cpp... topoldppc.top:7:20: error: ions.itp: No such file or directory cpp exit code: 256 Tried to execute: 'cpp -I/apps/gromacs/3.3/share/top topoldppc.top gromppzVWhWp' The 'cpp' command is defined in the .mdp file processing topology... Generated 1369 of the 2211 non-bonded parameter combinations Excluding 3 bonded neighbours for DPP 64 turning all bonds into constraints... Excluding 2 bonded neighbours for SOL 4152 turning all bonds into constraints... Cleaning up temporary file gromppzVWhWp --- Program grompp_mpi, VERSION 3.3 Source code file: toppush.c, line: 1264 Fatal error: No such moleculetype Mg --- Thanx for Using GROMACS - Have a Nice Day-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Re: error when running grompp
delara aghaie wrote: Dear Gromacs users I ahve a dppc monolayer on water layer 9tip4p-2005). I have added 8 Mg and 16 Cl ions using genion and now want to use grompp and then start the simulation to see the effect of ions on the pressure-area isotherm of the system. running grompp in gromacs 3.3 I see he following error: please help em to solve it.let me knoe please what is cpp? The C-preprocessor. In ancient Gromacs versions like this one, it was needed to interpret include, define, ifdef, etc. Your main problem is this: topoldppc.top:7:20: error: ions.itp: No such file or directory which then results in: --- Program grompp_mpi, VERSION 3.3 Source code file: toppush.c, line: 1264 Fatal error: No such moleculetype Mg --- Thanx for Using GROMACS - Have a Nice Day Either your #include statement in your .top is wrong or your cpp is nonfunctional, but I suspect the former. -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/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Probable error in trjcat; skipping frames
Dear gmx-users, I intended to concantanate two trajectories with no similar time frames i.e., both files have distinct time frames. But once I combine the files many time frames are skipped, details are as follows: File 1 has 2175 frames File 2 has 1232 frames I used the following command to concatenate: trjcat -f File1.xtc File2.xtc -o CombinedFile3.xtc Now I obtained in total 1266 frames instead of 3407 frames as expected. When I compared the CombinedFile3 with both File 1 and File 2, I found that it has somehow taken the first 34 frames from File 1 and rest of the frames belongs to File 2 i.e., the last file. I am unable to understand why trjcat skips the frames inspite of no similarity. I am using 4.5-beta version of Gromacs. I am also open to sharing the files, should that be needed. Any possible explanation as to why I am obtaining the combined trajectory with skipping frames, would be really helpful. Many Thanks, Lipi -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Probable error in trjcat; skipping frames
Lipi Thukral wrote: Dear gmx-users, I intended to concantanate two trajectories with no similar time frames i.e., both files have distinct time frames. But once I combine the files many time frames are skipped, details are as follows: File 1 has 2175 frames File 2 has 1232 frames What does gmxcheck tell you about each of these files? I used the following command to concatenate: trjcat -f File1.xtc File2.xtc -o CombinedFile3.xtc Now I obtained in total 1266 frames instead of 3407 frames as expected. When I compared the CombinedFile3 with both File 1 and File 2, I found that it has somehow taken the first 34 frames from File 1 and rest of the frames belongs to File 2 i.e., the last file. I am unable to understand why trjcat skips the frames inspite of no similarity. I am using 4.5-beta version of Gromacs. I am also open to sharing the files, should that be needed. There have been numerous beta versions over the last few years, none of which should necessarily be considered stable. Which beta are you using exactly? -Justin Any possible explanation as to why I am obtaining the combined trajectory with skipping frames, would be really helpful. Many Thanks, Lipi -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
RE: [gmx-users] Re: error when running grompp
I got the same error when doing the lysozyme tutorial on one of the machines provided by NERSC. the dept. of energy provided high performance computing service, specifically the carver machine. The gromacs default on that machine I think is also 3.*.*, so I'll go with the former also, namely #include statement. v/r, dc Date: Tue, 26 Apr 2011 16:23:52 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: [gmx-users] Re: error when running grompp delara aghaie wrote: Dear Gromacs users I ahve a dppc monolayer on water layer 9tip4p-2005). I have added 8 Mg and 16 Cl ions using genion and now want to use grompp and then start the simulation to see the effect of ions on the pressure-area isotherm of the system. running grompp in gromacs 3.3 I see he following error: please help em to solve it.let me knoe please what is cpp? The C-preprocessor. In ancient Gromacs versions like this one, it was needed to interpret include, define, ifdef, etc. Your main problem is this: topoldppc.top:7:20: error: ions.itp: No such file or directory which then results in: --- Program grompp_mpi, VERSION 3.3 Source code file: toppush.c, line: 1264 Fatal error: No such moleculetype Mg --- Thanx for Using GROMACS - Have a Nice Day Either your #include statement in your .top is wrong or your cpp is nonfunctional, but I suspect the former. -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 list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] how to define charge group?
Hi, I am trying to write a topology in gromacs format for a recently developed molecule in OPLS format. From the parameterization-paper, I know the partial charges on each of the atom in that molecule from the corresponding paper . But, I am not sure how to split the molecule topology into several charge-groups. I mean, is there any thumb-rule on how to define opls charge groups for using in gromacs. Only thing I know from mailing list is that one should not use large charge-groups. But, I was wondering if someone can provide some input on how to define charge-groups. Sanku-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] how to define charge group?
Sanku M wrote: Hi, I am trying to write a topology in gromacs format for a recently developed molecule in OPLS format. From the parameterization-paper, I know the partial charges on each of the atom in that molecule from the corresponding paper . But, I am not sure how to split the molecule topology into several charge-groups. I mean, is there any thumb-rule on how to define opls charge groups for using in gromacs. Only thing I know from mailing list is that one should not use large charge-groups. But, I was wondering if someone can provide some input on how to define charge-groups. Sanku Please read section 3.4.2 in the manual, particularly the Charge groups section. Charge groups need not have integral charge if using PME. -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/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] flexiable water - model
On 4/27/2011 1:29 AM, Nilesh Dhumal wrote: Hello, I am trying to run a simulation for flexiable water. I use the parameters from J. Chem. Phys. (2006),124,024503 paper and made floowing changes. I addes WAT as a new residue name in aminoacids.dat I addred two atom times in ffoplsaa.atp opls_1001 15.99940 ; O SPC_fw Water opls_10021.00800 ; H SPC_fw Water I added following parameters in ffoplsaa.rtp [ WAT] [ atoms ] OWA opls_1001 -0.82 1 HWA1 opls_1002 0.41 2 HWA2 opls_1002 0.41 2 [ bonds ] OWA HWA1 OWA HWA2 I made a spc_fw.itp file. ; Derived from parsing of runfiles/alat.top.orig [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ ;1 3 yes 0.5 0.5 ; comb-rule 3 is square-root sigma, the OPLSAA version This is a wrong approach. You should model your .itp file on the existing standard water .itp files. They are designed so that you can simply #include them in other topologies from the right places. Yours cannot be used in this way, because you have erroneously used a [defaults] directive (which can only appear once in a topology). You should #include the main force field files, then #include a properly-formed spc_fw.itp for the atom, bond and molecule types, then specify your [molecules], as Justin said. Mark [ atomtypes ] ; full atom descriptions are available in ffoplsaa.atp ; name bond_typemasscharge ptype sigma epsilon opls_1001 OWA 815.99940 -0.820 A3.1655e-01 6.503e-01 opls_1002 HWA 1 1.00800 0.410 A0.00e+00 0.00e+00 [ bondtypes ] ; ij func b0 kb OWAHWA 10.1012 443153.3808 ; J. Chem. Phys. (2006),124,024503 [ angletypes ] ; ijk func th0 cth HWA OWA HWA 1 113.24 317.5656 ; J. Chem. Phys. (2006),124,024503 [ moleculetype ] ; Namenrexcl WAT 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 1 opls_1001 1WAT OWA 1 -0.82 2 opls_1002 1WATHWA1 1 0.41 3 opls_1002 1WATHWA2 1 0.41 [ bonds ] ; i j funct 1 2 1 1 3 1 [ angles ] ; i j k funct 2 1 3 1 Finally I made changes in ffoplsaa.itp file ;#include ffoplsaanb.itp ;#include ffoplsaabon.itp #include spc_fw.itp #include spc_fw_mol.itp For pdb2gmx pdb2gmx -f water.pdb -o water.pdb -p water.top -ter I get following error Fatal error: Atom OWA in residue HOH 1 not found in rtp entry with 3 atoms while sorting atoms WHy is reading HOH residue. In my pdb file I mentioned WAT as residure. How can I fix this error? 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/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] error when running grompp
On 4/27/2011 6:21 AM, delara aghaie wrote: Dear Gromacs users I ahve a dppc monolayer on water layer 9tip4p-2005). I have added 8 Mg and 16 Cl ions using genion and now want to use grompp and then start the simulation to see the effect of ions on the pressure-area isotherm of the system. running grompp in gromacs 3.3 I see he following error: Unless you have an important reason of continuity for using GROMACS 3.3, you will get much better performance from the latest GROMACS version. Mark please help em to solve it.let me knoe please what is cpp? Thanks in advance D. Aghaie -bash-3.2$ grompp_mpi -c dppc-salt-Mg-0.1.gro -f run.mdp -n indexsalt-Mg.ndx -p topoldppc.top -o topol.tpr -np 8 :-) G R O M A C S (-: Groningen Machine for Chemical Simulation :-) VERSION 3.3 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2004, The GROMACS development team, check out http://www.gromacs.orgfor more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) grompp_mpi (-: Option Filename Type Description -frun.mdp Input, Opt! grompp input file with MD parameters -po mdout.mdp Output grompp input file with MD parameters -c dppc-salt-Mg-0.1.gro InputGeneric structure: gro g96 pdb tpr tpb tpa xml -r conf.gro Input, Opt. Generic structure: gro g96 pdb tpr tpb tpa xml -rb conf.gro Input, Opt. Generic structure: gro g96 pdb tpr tpb tpa xml -n indexsalt-Mg.ndx Input, Opt! Index file -deshuf deshuf.ndx Output, Opt. Index file -p topoldppc.top InputTopology file -pp processed.top Output, Opt. Topology file -o topol.tpr Output Generic run input: tpr tpb tpa xml -t traj.trr Input, Opt. Full precision trajectory: trr trj -e ener.edr Input, Opt. Generic energy: edr ene Option Type Value Description -- -[no]h bool no Print help info and quit -[no]X bool no Use dialog box GUI to edit command line options -niceint 0 Set the nicelevel -[no]v boolyes Be loud and noisy -time real -1 Take frame at or first after this time. -npint 8 Generate statusfile for # nodes -[no]shuffle bool no Shuffle molecules over nodes -[no]sort bool no Sort molecules according to X coordinate -[no]rmvsbds boolyes Remove constant bonded interactions with virtual sites -load string Releative load capacity of each node on a parallel machine. Be sure to use quotes around the string, which should contain a number for each node -maxwarnint 10 Number of warnings after which input processing stops -[no]check14 bool no Remove 1-4 interactions without Van der Waals -[no]renum boolyes Renumber atomtypes and minimize number of atomtypes creating statusfile for 8 nodes... Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1# checking input for internal consistency... calling cpp... topoldppc.top:7:20: error: ions.itp: No such file or directory cpp exit code: 256 Tried to execute: 'cpp -I/apps/gromacs/3.3/share/top topoldppc.top gromppzVWhWp' The 'cpp' command is defined in the .mdp file processing topology... Generated 1369 of the 2211 non-bonded parameter combinations Excluding 3 bonded neighbours for DPP 64 turning all bonds into constraints... Excluding 2 bonded neighbours for SOL 4152 turning all bonds into constraints... Cleaning up temporary file gromppzVWhWp --- Program grompp_mpi, VERSION 3.3 Source code file: toppush.c, line: 1264 Fatal error: No such moleculetype Mg --- Thanx for Using GROMACS - Have a Nice Day -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Placing anion/cation at a particular distance from peptide
On 4/27/2011 5:13 AM, shivangi nangia wrote: Dear gmx users, I need to design a starting configuration of a polypeptide with charged side chains sitting in a box of water with Cl- ions within 7 ang of its radius. I realize that in such a system like charges will essentially prefer to be as far as possible from each other, but I still need the above stated configuration. Is there an easy way to specify the distance of the anions to be added from the peptide ? No. You will have to find water molecules a suitable distance from your solute and replace them by hand (and update your .top accordingly). 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/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Is it flexible water or all the bond, angle fixed? what is the potential energy in Gromacs 4.5 using OPLSAA
Hi gromacs experts, I used gromacs 4.5.3. my system has only spce water, no other types. In .mdp file, I used the following parameters; define = constraints = none constraint-algorithm = Lincs Can u tell me Is it flexible water or all the bond, angle fixed using the above setting? what is the equations of potential energy in Gromacs 4.5 using OPLSAA? Best regards-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Is it flexible water or all the bond, angle fixed? what is the potential energy in Gromacs 4.5 using OPLSAA
MD wrote: Hi gromacs experts, I used gromacs 4.5.3. my system has only spce water, no other types. In .mdp file, I used the following parameters; define = constraints = none constraint-algorithm = Lincs Can u tell me Is it flexible water or all the bond, angle fixed using the above setting? Look at spce.itp and/or your md.log file. If the #ifdef FLEXIBLE statement is not invoked, the SETTLE algorithm is used. what is the equations of potential energy in Gromacs 4.5 using OPLSAA? The components of various functional forms are described in the manual. -Justin Best regards 体验网易邮箱2G超大附件，轻松发优质大电影、大照片，提速3倍! http://mail.163.com/html/110414_attachment/att1.htm -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Re:gmx-users Digest, Vol 84, Issue 207
Hi Justin,
When i define
define = FLEXIBLE
constraints = none
constraint-algorithm = Lincs
I saw my .log file.
Input Parameters:
integrator = md
nsteps = 1
init_step= 0
ns_type = Grid
nstlist = 5
ndelta = 2
nstcomm = 1
comm_mode= Linear
nstlog = 50
nstxout = 0
nstvout = 0
nstfout = 0
nstenergy= 50
nstxtcout= 50
init_t = 0
delta_t = 0.002
xtcprec = 1000
nkx = 0
nky = 0
nkz = 0
pme_order= 4
ewald_rtol = 1e-05
ewald_geometry = 0
epsilon_surface = 0
optimize_fft = FALSE
ePBC = xyz
bPeriodicMols= FALSE
bContinuation= FALSE
bShakeSOR= FALSE
etc = Berendsen
epc = Berendsen
epctype = Isotropic
tau_p= 0.5
ref_p (3x3):
ref_p[0]={ 1.0e+00, 0.0e+00, 0.0e+00}
ref_p[1]={ 0.0e+00, 1.0e+00, 0.0e+00}
ref_p[2]={ 0.0e+00, 0.0e+00, 1.0e+00}
compress (3x3):
compress[0]={ 4.5e-05, 0.0e+00, 0.0e+00}
compress[1]={ 0.0e+00, 4.5e-05, 0.0e+00}
compress[2]={ 0.0e+00, 0.0e+00, 4.5e-05}
refcoord_scaling = No
posres_com (3):
posres_com[0]= 0.0e+00
posres_com[1]= 0.0e+00
posres_com[2]= 0.0e+00
posres_comB (3):
posres_comB[0]= 0.0e+00
posres_comB[1]= 0.0e+00
posres_comB[2]= 0.0e+00
andersen_seed= 815131
rlist= 0.9
rtpi = 0.05
coulombtype = Cut-off
rcoulomb_switch = 0
rcoulomb = 0.9Input Parameters:
integrator = md
nsteps = 1
init_step= 0
ns_type = Grid
nstlist = 5
ndelta = 2
nstcomm = 1
comm_mode= Linear
nstlog = 50
nstxout = 0
nstvout = 0
nstfout = 0
nstenergy= 50
nstxtcout= 50
init_t = 0
delta_t = 0.002
xtcprec = 1000
nkx = 0
nky = 0
nkz = 0
pme_order= 4
ewald_rtol = 1e-05
ewald_geometry = 0
epsilon_surface = 0
optimize_fft = FALSE
ePBC = xyz
bPeriodicMols= FALSE
bContinuation= FALSE
bShakeSOR= FALSE
etc = Berendsen
epc = Berendsen
epctype = Isotropic
tau_p= 0.5
ref_p (3x3):
ref_p[0]={ 1.0e+00, 0.0e+00, 0.0e+00}
ref_p[1]={ 0.0e+00, 1.0e+00, 0.0e+00}
ref_p[2]={ 0.0e+00, 0.0e+00, 1.0e+00}
compress (3x3):
compress[0]={ 4.5e-05, 0.0e+00, 0.0e+00}
compress[1]={ 0.0e+00, 4.5e-05, 0.0e+00}
compress[2]={ 0.0e+00, 0.0e+00, 4.5e-05}
refcoord_scaling = No
posres_com (3):
posres_com[0]= 0.0e+00
posres_com[1]= 0.0e+00
posres_com[2]= 0.0e+00
posres_comB (3):
posres_comB[0]= 0.0e+00
posres_comB[1]= 0.0e+00
posres_comB[2]= 0.0e+00
andersen_seed= 815131
vdwtype = Cut-off
rvdw_switch = 0
rvdw = 0.9
epsilon_r= 1
epsilon_rf = 1
tabext = 1
implicit_solvent = No
gb_algorithm = Still
gb_epsilon_solvent = 80
nstgbradii = 1
rgbradii = 2
gb_saltconc = 0
gb_obc_alpha = 1
gb_obc_beta = 0.8
gb_obc_gamma = 4.85
sa_surface_tension = 2.092
DispCorr = EnerPres
free_energy = no
init_lambda = 0
sc_alpha = 0
sc_power = 0
sc_sigma = 0.3
delta_lambda = 0
nwall= 0
wall_type= 9-3
wall_atomtype[0] = -1
wall_atomtype[1] = -1
wall_density[0] = 0
wall_density[1] = 0
wall_ewald_zfac = 3
pull = no
disre= No
disre_weighting = Conservative
disre_mixed = FALSE
dr_fc= 1000
dr_tau = 0
nstdisreout = 100
orires_fc= 0
orires_tau = 0
nstorireout = 100
dihre-fc = 1000
em_stepsize = 0.01
em_tol
Re: [gmx-users] Re:gmx-users Digest, Vol 84, Issue 207
On 4/27/2011 11:52 AM, MD wrote:
Hi Justin,
When i define
define = FLEXIBLE
This is not of the correct form.
constraints = none
constraint-algorithm = Lincs
I saw my .log file.
Input Parameters:
integrator = md
nsteps = 1
init_step = 0
ns_type = Grid
nstlist = 5
ndelta = 2
nstcomm = 1
comm_mode = Linear
nstlog = 50
nstxout = 0
nstvout = 0
nstfout = 0
nstenergy = 50
nstxtcout = 50
init_t = 0
delta_t = 0.002
xtcprec = 1000
nkx = 0
nky = 0
nkz = 0
pme_order = 4
ewald_rtol = 1e-05
ewald_geometry = 0
epsilon_surface = 0
optimize_fft = FALSE
ePBC = xyz
bPeriodicMols = FALSE
bContinuation = FALSE
bShakeSOR = FALSE
etc = Berendsen
epc = Berendsen
epctype = Isotropic
tau_p = 0.5
ref_p (3x3):
ref_p[ 0]={ 1.0e+00, 0.0e+00, 0.0e+00}
ref_p[ 1]={ 0.0e+00, 1.0e+00, 0.0e+00}
ref_p[ 2]={ 0.0e+00, 0.0e+00, 1.0e+00}
compress (3x3):
compress[ 0]={ 4.5e-05, 0.0e+00, 0.0e+00}
compress[ 1]={ 0.0e+00, 4.5e-05, 0.0e+00}
compress[ 2]={ 0.0e+00, 0.0e+00, 4.5e-05}
refcoord_scaling = No
posres_com (3):
posres_com[0]= 0.0e+00
posres_com[1]= 0.0e+00
posres_com[2]= 0.0e+00
posres_comB (3):
posres_comB[0]= 0.0e+00
posres_comB[1]= 0.0e+00
posres_comB[2]= 0.0e+00
andersen_seed = 815131
rlist = 0.9
rtpi = 0.05
coulombtype = Cut-off
rcoulomb_switch = 0
rcoulomb = 0.9Input Parameters:
integrator = md
nsteps = 1
init_step = 0
ns_type = Grid
nstlist = 5
ndelta = 2
nstcomm = 1
comm_mode = Linear
nstlog = 50
nstxout = 0
nstvout = 0
nstfout = 0
nstenergy = 50
nstxtcout = 50
init_t = 0
delta_t = 0.002
xtcprec = 1000
nkx = 0
nky = 0
nkz = 0
pme_order = 4
ewald_rtol = 1e-05
ewald_geometry = 0
epsilon_surface = 0
optimize_fft = FALSE
ePBC = xyz
bPeriodicMols = FALSE
bContinuation = FALSE
bShakeSOR = FALSE
etc = Berendsen
epc = Berendsen
epctype = Isotropic
tau_p = 0.5
ref_p (3x3):
ref_p[ 0]={ 1.0e+00, 0.0e+00, 0.0e+00}
ref_p[ 1]={ 0.0e+00, 1.0e+00, 0.0e+00}
ref_p[ 2]={ 0.0e+00, 0.0e+00, 1.0e+00}
compress (3x3):
compress[ 0]={ 4.5e-05, 0.0e+00, 0.0e+00}
compress[ 1]={ 0.0e+00, 4.5e-05, 0.0e+00}
compress[ 2]={ 0.0e+00, 0.0e+00, 4.5e-05}
refcoord_scaling = No
posres_com (3):
posres_com[0]= 0.0e+00
posres_com[1]= 0.0e+00
posres_com[2]= 0.0e+00
posres_comB (3):
posres_comB[0]= 0.0e+00
posres_comB[1]= 0.0e+00
posres_comB[2]= 0.0e+00
andersen_seed = 815131
vdwtype = Cut-off
rvdw_switch = 0
rvdw = 0.9
epsilon_r = 1
epsilon_rf = 1
tabext = 1
implicit_solvent = No
gb_algorithm = Still
gb_epsilon_solvent = 80
nstgbradii = 1
rgbradii = 2
gb_saltconc = 0
gb_obc_alpha = 1
gb_obc_beta = 0.8
gb_obc_gamma = 4.85
sa_surface_tension = 2.092
DispCorr = EnerPres
free_energy = no
init_lambda = 0
sc_alpha = 0
sc_power = 0
sc_sigma = 0.3
delta_lambda = 0
nwall = 0
wall_type = 9-3
wall_atomtype[0] = -1
wall_atomtype[1] = -1
wall_density[0] = 0
wall_density[1] = 0
wall_ewald_zfac = 3
pull = no
disre = No
disre_weighting = Conservative
disre_mixed = FALSE
dr_fc = 1000
dr_tau = 0
nstdisreout = 100
orires_fc = 0
orires_tau = 0
nstorireout = 100
dihre-fc = 1000
em_stepsize = 0.01
em_tol = 100
niter = 20
fc_stepsize = 0
nstcgsteep = 1000
nbfgscorr = 10
ConstAlg = Lincs
shake_tol = 0.0001
lincs_order = 4
lincs_warnangle = 30
lincs_iter = 1
bd_fric = 0
ld_seed = 1993
cos_accel = 0
deform (3x3):
deform[ 0]={ 0.0e+00, 0.0e+00, 0.0e+00}
deform[ 1]={ 0.0e+00, 0.0e+00, 0.0e+00}
deform[ 2]={ 0.0e+00, 0.0e+00, 0.0e+00}
userint1 = 0
userint2 = 0
userint3 = 0
userint4 = 0
userreal1 = 0
userreal2 = 0
userreal3 = 0
userreal4 = 0
grpopts:
nrdf: 1941
ref_t: 300
tau_t: 0.1
anneal: No
ann_npoints: 0
acc: 0 0 0
nfreeze: N N N
energygrp_flags[ 0]: 0
efield-x:
n = 0
efield-xt:
n = 0
efield-y:
n = 0
efield-yt:
n = 0
efield-z:
n = 0
efield-zt:
n = 0
bQMMM = FALSE
QMconstraints = 0
QMMMscheme = 0
scalefactor = 1
qm_opts:
ngQM = 0
Table routines are used for coulomb: FALSE
Table routines are used for vdw: FALSE
Cut-off's: NS: 0.9 Coulomb: 0.9 LJ: 0.9
System total charge: 0.000
Enabling SPC water optimization for 216 molecules.
Configuring nonbonded kernels...
Testing AMD 3DNow support... not present.
Testing ia32 SSE support... present.
However if i
define =
constraints = none
constraint-algorithm = Lincs
The .log file is similar to the above .log file. So i can not know whether the
constraints invoked.
I think you haven't looked far enough. Algorithms being used that are
important enough to have names and literature citations are referred to
by those in the .log file. Read and learn :-)
Is it only SETTLE algorithm for water models in Gromacs 4.5.3?
Have you looked in the manual?
Mark
MD wrote:
Hi gromacs experts,
I used gromacs 4.5.3. my system has only spce water, no other types.
In .mdp file,
I used the following parameters;
define =
constraints = none
constraint-algorithm = Lincs
Can u tell me Is it
[gmx-users] trjconv
Hello dear user, after 5ns MD,I used trjconv -f -s -pbc -mol -center -o *.pdb command to get the whole protein without any separation,but I found some part of the residue was broken,and some new bond at the end of some residue was formed.I need the intact molecule for docking,but how should I solve this problem. any advice was appreciate. tanks,-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Urey-Bradley constant in CHARMM to GMX
The Urey Bradley constant in CHARMM is expressed in units of kcal per (mol squared angstrom). However, in the Gromacs manual in Table 5.5, it is expressed in kJ/mol. How do we convert the constant from kcal per (mol squared angstrom) to kJ/mol in gromacs. Could gromacs have been expressing this constant in kJ per (mol squared nanometers) rather than in kJ/mol. Thanks, Bernard-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Re: Probable error in trjcat; skipping frames
Hi Justin, I am using Gromacs 4.5 beta-2. gmxcheck with file 1 and file 2 tells me exactly the number of frames I specified. gmxcheck -f File1.xtc Frames: 2175 gmxcheck -f File2.xtc Frames: 1232 While after concatenating, it skips the frames and the combined trajectory results in 1266 frames. Do you attribute this to Gromacs4.5beta2 version? Is there a possible bug in that version for trjcat? Regards, Lipi Lipi Thukral wrote: Dear gmx-users, I intended to concantanate two trajectories with no similar time frames i.e., both files have distinct time frames. But once I combine the files many time frames are skipped, details are as follows: File 1 has 2175 frames File 2 has 1232 frames What does gmxcheck tell you about each of these files? I used the following command to concatenate: trjcat -f File1.xtc File2.xtc -o CombinedFile3.xtc Now I obtained in total 1266 frames instead of 3407 frames as expected. When I compared the CombinedFile3 with both File 1 and File 2, I found that it has somehow taken the first 34 frames from File 1 and rest of the frames belongs to File 2 i.e., the last file. I am unable to understand why trjcat skips the frames inspite of no similarity. I am using 4.5-beta version of Gromacs. I am also open to sharing the files, should that be needed. There have been numerous beta versions over the last few years, none of which should necessarily be considered stable. Which beta are you using exactly? -Justin Any possible explanation as to why I am obtaining the combined trajectory with skipping frames, would be really helpful. Many Thanks, Lipi -- 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 On 26 April 2011 22:41, Lipi Thukral lipi.thuk...@gmail.com wrote: Dear gmx-users, I intended to concantanate two trajectories with no similar time frames i.e., both files have distinct time frames. But once I combine the files many time frames are skipped, details are as follows: File 1 has 2175 frames File 2 has 1232 frames I used the following command to concatenate: trjcat -f File1.xtc File2.xtc -o CombinedFile3.xtc Now I obtained in total 1266 frames instead of 3407 frames as expected. When I compared the CombinedFile3 with both File 1 and File 2, I found that it has somehow taken the first 34 frames from File 1 and rest of the frames belongs to File 2 i.e., the last file. I am unable to understand why trjcat skips the frames inspite of no similarity. I am using 4.5-beta version of Gromacs. I am also open to sharing the files, should that be needed. Any possible explanation as to why I am obtaining the combined trajectory with skipping frames, would be really helpful. Many Thanks, Lipi -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
