Re: [gmx-users] Re: Chloroform (CHCl3) solvent box for G53a5 force field
Pablo Englebienne wrote: Thanks for the suggestions, Justin. I'm still having issues with instabilities and large fluctuations in unconstrained NPT simulations of the CHCl3 box, so I'll appreciate comments from the list on my run parameters. I think there is a problem with the pressure coupling, but I'm not sure what to change to fix it. I modified the topology, using the H-Cl and Cl-Cl as bonds, and the H-C and C-Cl bond distances as constraints: ---[chcl3.itp]--- [...] [ bonds ] 1 3 2gb_47 1 4 2gb_47 1 5 2gb_47 3 4 2gb_48 3 5 2gb_48 4 5 2gb_48 [ constraints ] 1 2 10.1100 2 3 10.1758 2 4 10.1758 2 5 10.1758 [...] ---[chcl3.itp]--- This prevented the grompp warning message about too many constraints to appear. I first minimized the 216-molecule box with the following mdp: ---[em.mdp]--- integrator = steep nsteps = 5 emtol = 100 emstep = 0.01 ; ;Electrostatics ; coulombtype = PME rlist = 1 rcoulomb= 1.0 ns_type = grid nstlist = 1 ; ;vdW ; rvdw= 1.0 ; ; PBC ; pbc= xyz ; ; constraints ; constraint_algorithm = lincs constraints = none lincs_iter= 1 lincs_order= 4 ---[em.mdp]--- This converged well: ---[em.log]--- Energies (kJ/mol) G96Bond G96AngleLJ (SR) Coulomb (SR) Coul. recip. 3.05135e+004.35449e-01 -5.41548e+03 -2.09196e+01 -2.57100e+01 Potential Pressure (bar) Cons. rmsd () -5.45863e+031.17031e+031.50663e-07 Steepest Descents converged to Fmax < 100 in 297 steps Potential Energy = -5.45862698325888e+03 Maximum force = 9.95795243267423e+01 on atom 798 Norm of force = 3.22657158607021e+01 ---[em.log]--- Then, I heated the system to 300K in an NVT simulation: ---[nvt.mdp]--- ; ;NVT equilibration ; ; Run parameters integrator= md nsteps= 25000 dt= 0.002 ; Output control nstxout= 100 nstvout= 100 nstenergy= 100 nstlog= 100 ; Bond parameters continuation= no constraint_algorithm = lincs constraints = none lincs_iter= 1 lincs_order= 4 ; Neighborsearching ns_type= grid nstlist= 5 rlist= 1.0 rcoulomb= 1.0 rvdw= 1.0 ; Electrostatics coulombtype= PME pme_order= 4 fourierspacing= 0.16 ; Temperature coupling is on tcoupl= V-rescale tau_t= 0.1 tc_grps= SYSTEMref_t= 300 ; Pressure coupling is off pcoupl= no; PBC pbc= xyz ; Dispersion correction DispCorr= EnerPres ; Velocity generation gen_vel= yes gen_temp= 300 gen_seed= -1 ---[nvt.mdp]--- This simulation yielded a temperature with large fluctuations: Energy Average RMSD Fluct. Drift Tot-Drift --- Temperature 298.89910.185710.1724 -0.0360483 -1.80249 The fluctuations look fairly large, but I'm not sure if these are reasonable for a 216-molecule system. I then applied pressure to the system: ---[npt.mdp]--- ; NPT equilibration ; Run parameters integrator= md nsteps= 5 dt= 0.002 ; Output control nstxout= 100 nstvout= 100 nstenergy= 100 nstlog= 100 ; Bond parameters continuation= yes constraint_algorithm = lincs constraints= none lincs_iter= 1 lincs_order= 4 ; Neighborsearching ns_type= grid nstlist= 5 rlist= 1.0 rcoulomb= 1.0 rvdw= 1.0 ; Electrostatics coulombtype= PME pme_order= 4 fourierspacing= 0.16 ; Temperature coupling is on tcoupl= V-rescale tc-grps= SYSTEM tau_t= 0.1 ref_t= 300 ; Pressure coupling is on pcoupl= Parrinello-Rahman pcoupltype= isotropic tau_p= 2.0 ref_p= 1.0 compressibility = 1e-4 ; Periodic boundary conditions pbc= xyz ; Dispersion correction DispCorr= EnerPres ; Velocity generation gen_vel= no ---[npt.mdp]--- This simulation yields large fluctuations of temperature as well: I tried playing around with the value of tau_p: - tau_p = 5.0 ==> slow increase of density, not stable after 100 ps; temperature with similar fluctuations as NVT (300K, RMSD 9); pressure starts oscillating wildly after ~10 ps - tau_p = 2.0 ==> increase of density, not stable at end of simulation; huge fluctuations in potential
[gmx-users] Re: Chloroform (CHCl3) solvent box for G53a5 force field
Thanks for the suggestions, Justin. I'm still having issues with instabilities and large fluctuations in unconstrained NPT simulations of the CHCl3 box, so I'll appreciate comments from the list on my run parameters. I think there is a problem with the pressure coupling, but I'm not sure what to change to fix it. I modified the topology, using the H-Cl and Cl-Cl as bonds, and the H-C and C-Cl bond distances as constraints: ---[chcl3.itp]--- [...] [ bonds ] 1 3 2gb_47 1 4 2gb_47 1 5 2gb_47 3 4 2gb_48 3 5 2gb_48 4 5 2gb_48 [ constraints ] 1 2 10.1100 2 3 10.1758 2 4 10.1758 2 5 10.1758 [...] ---[chcl3.itp]--- This prevented the grompp warning message about too many constraints to appear. I first minimized the 216-molecule box with the following mdp: ---[em.mdp]--- integrator = steep nsteps = 5 emtol = 100 emstep = 0.01 ; ;Electrostatics ; coulombtype = PME rlist = 1 rcoulomb= 1.0 ns_type = grid nstlist = 1 ; ;vdW ; rvdw= 1.0 ; ; PBC ; pbc= xyz ; ; constraints ; constraint_algorithm = lincs constraints = none lincs_iter= 1 lincs_order= 4 ---[em.mdp]--- This converged well: ---[em.log]--- Energies (kJ/mol) G96Bond G96AngleLJ (SR) Coulomb (SR) Coul. recip. 3.05135e+004.35449e-01 -5.41548e+03 -2.09196e+01 -2.57100e+01 Potential Pressure (bar) Cons. rmsd () -5.45863e+031.17031e+031.50663e-07 Steepest Descents converged to Fmax < 100 in 297 steps Potential Energy = -5.45862698325888e+03 Maximum force = 9.95795243267423e+01 on atom 798 Norm of force = 3.22657158607021e+01 ---[em.log]--- Then, I heated the system to 300K in an NVT simulation: ---[nvt.mdp]--- ; ;NVT equilibration ; ; Run parameters integrator= md nsteps= 25000 dt= 0.002 ; Output control nstxout= 100 nstvout= 100 nstenergy= 100 nstlog= 100 ; Bond parameters continuation= no constraint_algorithm = lincs constraints= none lincs_iter= 1 lincs_order= 4 ; Neighborsearching ns_type= grid nstlist= 5 rlist= 1.0 rcoulomb= 1.0 rvdw= 1.0 ; Electrostatics coulombtype= PME pme_order= 4 fourierspacing= 0.16 ; Temperature coupling is on tcoupl= V-rescale tau_t= 0.1 tc_grps= SYSTEM ref_t= 300 ; Pressure coupling is off pcoupl= no ; PBC pbc= xyz ; Dispersion correction DispCorr= EnerPres ; Velocity generation gen_vel= yes gen_temp= 300 gen_seed= -1 ---[nvt.mdp]--- This simulation yielded a temperature with large fluctuations: Energy Average RMSD Fluct. Drift Tot-Drift --- Temperature 298.89910.185710.1724 -0.0360483 -1.80249 The fluctuations look fairly large, but I'm not sure if these are reasonable for a 216-molecule system. I then applied pressure to the system: ---[npt.mdp]--- ; NPT equilibration ; Run parameters integrator= md nsteps= 5 dt= 0.002 ; Output control nstxout= 100 nstvout= 100 nstenergy= 100 nstlog= 100 ; Bond parameters continuation= yes constraint_algorithm = lincs constraints= none lincs_iter= 1 lincs_order= 4 ; Neighborsearching ns_type= grid nstlist= 5 rlist= 1.0 rcoulomb= 1.0 rvdw= 1.0 ; Electrostatics coulombtype= PME pme_order= 4 fourierspacing= 0.16 ; Temperature coupling is on tcoupl= V-rescale tc-grps= SYSTEM tau_t= 0.1 ref_t= 300 ; Pressure coupling is on pcoupl= Parrinello-Rahman pcoupltype= isotropic tau_p= 2.0 ref_p= 1.0 compressibility = 1e-4 ; Periodic boundary conditions pbc= xyz ; Dispersion correction DispCorr= EnerPres ; Velocity generation gen_vel= no ---[npt.mdp]--- This simulation yields large fluctuations of temperature as well: I tried playing around with the value of tau_p: - tau_p = 5.0 ==> slow increase of density, not stable after 100 ps; temperature with similar fluctuations as NVT (300K, RMSD 9); pressure starts oscillating wildly after ~10 ps - tau_p = 2.0 ==> increase of density, not stable at end of simulation; huge fluctuation
Re: [gmx-users] Re: Chloroform (CHCl3) solvent box for G53a5 force field
Pablo Englebienne wrote: Following up on the previous message, I noticed that the topology I previously sent (including 10 bonds) works for a minimization, but not for an MD simulation. grompp issues the following warning: WARNING 1 [file topol.top, line 29]: Molecule type 'CHCL3' has 10 constraints. For stability and efficiency there should not be more constraints than internal number of degrees of freedom: 9. I therefore used the following .itp file, with only the C-H and C-Cl bonds: If bonds are supposed to be defined between, i.e. H-Cl and Cl-Cl, then this may not be appropriate. Instead, you could perhaps set the covalent bonds as [constraints] in the topology, leaving the other "nonbonded" bonds as [bonds] (and then use "constraints = none" in the .mdp file, so only the [constraints] are used). --[chcl3.itp]-- [ moleculetype ] ; Namenrexcl CHCL3 1 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeBchargeB massB 1 HCHL 1 CHCL3 HChL 1 0.082 1.008 2 CCHL 1 CHCL3 CChL 1 0.179 12.011 3 CLCHL 1 CHCL3 CLCh1 1 -0.087 35.453 4 CLCHL 1 CHCL3 CLCh2 1 -0.087 35.453 5 CLCHL 1 CHCL3 CLCh3 1 -0.087 35.453 [ bonds ] ; aiaj functc0c1c2c3 1 2 2gb_39 2 3 2gb_40 2 4 2gb_40 2 5 2gb_40 [ angles ] ; aiajak functc0c1 c2c3 1 2 3 2 ga_43 1 2 4 2 ga_43 1 2 5 2 ga_43 3 2 4 2 ga_44 3 2 5 2 ga_44 4 2 5 2 ga_44 [ exclusions ] 1 2 3 4 5 2 1 3 4 5 3 1 2 4 5 4 1 2 3 5 5 1 2 3 4 --[chcl3.itp]-- These are the steps I took: - build a box with 216 CHCL3 molecules with genbox - adjusted the density to 1479 with editconf - minimized the box to F<100 (steep, 5 steps) - equilibrated NVT (position restrained C), 100ps, 300K, tau_t 0.1 - equilibrated NPT (position restrained C), 100ps, 300K, 1bar, tau_t 0.1, tau_p 2.0, compressibility 1e-4 (from CRC handbook) What is the purpose of position restraints here? Until here, everything looks decent, except for relatively large fluctuations in T (RMSD ~9K) and density (RMSD ~10kg m-3). Probably a consequence of restraining the starting structure. I'd say you're not equilibrating appropriately with position restraints imposed. I then performed an unconstrained MD, 1ns, otherwise identical parameters to NPT equilibration. Temp (300K) and density (1450 kg m-3) stable, but fluctuating (RMSD 8 and 20 respectively). In order to compare the results with Tironi and van Gunsteren, Molecular Physics 1994, 83, 381, who used the same GROMOS parameters: Epot = -28.6 +/- 0.3 kJ/mol, density 1520 +/- 12 kg m-3. This is the output I get from g_energy: Energy Average RMSD Fluct. Drift Tot-Drift --- Potential -4720.16119.141118.978 -0.0215895 -21.5896 Therefore molar Epot = -(-4720)/216 = 21.9 kJ/mol. What factors could be accountable for the decrease wrt the reported value of 28.4? Experimental deltaHv is 31.4 kJ/mol (same reference). Insufficient equilibration, and a variety of factors within the .mdp file. If you want feedback on run parameters, you'll have to post the .mdp. -Justin Would there be any other parameters I should check before using this solvent box in production runs? Regards, Pablo -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: Chloroform (CHCl3) solvent box for G53a5 force field
Following up on the previous message, I noticed that the topology I previously sent (including 10 bonds) works for a minimization, but not for an MD simulation. grompp issues the following warning: WARNING 1 [file topol.top, line 29]: Molecule type 'CHCL3' has 10 constraints. For stability and efficiency there should not be more constraints than internal number of degrees of freedom: 9. I therefore used the following .itp file, with only the C-H and C-Cl bonds: --[chcl3.itp]-- [ moleculetype ] ; Namenrexcl CHCL3 1 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeBchargeB massB 1 HCHL 1 CHCL3 HChL 1 0.082 1.008 2 CCHL 1 CHCL3 CChL 1 0.179 12.011 3 CLCHL 1 CHCL3 CLCh1 1 -0.087 35.453 4 CLCHL 1 CHCL3 CLCh2 1 -0.087 35.453 5 CLCHL 1 CHCL3 CLCh3 1 -0.087 35.453 [ bonds ] ; aiaj functc0c1c2c3 1 2 2gb_39 2 3 2gb_40 2 4 2gb_40 2 5 2gb_40 [ angles ] ; aiajak functc0c1 c2c3 1 2 3 2 ga_43 1 2 4 2 ga_43 1 2 5 2 ga_43 3 2 4 2 ga_44 3 2 5 2 ga_44 4 2 5 2 ga_44 [ exclusions ] 1 2 3 4 5 2 1 3 4 5 3 1 2 4 5 4 1 2 3 5 5 1 2 3 4 --[chcl3.itp]-- These are the steps I took: - build a box with 216 CHCL3 molecules with genbox - adjusted the density to 1479 with editconf - minimized the box to F<100 (steep, 5 steps) - equilibrated NVT (position restrained C), 100ps, 300K, tau_t 0.1 - equilibrated NPT (position restrained C), 100ps, 300K, 1bar, tau_t 0.1, tau_p 2.0, compressibility 1e-4 (from CRC handbook) Until here, everything looks decent, except for relatively large fluctuations in T (RMSD ~9K) and density (RMSD ~10kg m-3). I then performed an unconstrained MD, 1ns, otherwise identical parameters to NPT equilibration. Temp (300K) and density (1450 kg m-3) stable, but fluctuating (RMSD 8 and 20 respectively). In order to compare the results with Tironi and van Gunsteren, Molecular Physics 1994, 83, 381, who used the same GROMOS parameters: Epot = -28.6 +/- 0.3 kJ/mol, density 1520 +/- 12 kg m-3. This is the output I get from g_energy: Energy Average RMSD Fluct. Drift Tot-Drift --- Potential -4720.16119.141118.978 -0.0215895 -21.5896 Therefore molar Epot = -(-4720)/216 = 21.9 kJ/mol. What factors could be accountable for the decrease wrt the reported value of 28.4? Experimental deltaHv is 31.4 kJ/mol (same reference). Would there be any other parameters I should check before using this solvent box in production runs? Regards, Pablo -- Pablo Englebienne, PhD Institute of Complex Molecular Systems (ICMS) Eindhoven University of Technology, TU/e PO Box 513, HG -1.26 5600 MB Eindhoven, The Netherlands Tel +31 40 247 5349 ___ 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: Chloroform (CHCl3) solvent box for G53a5 force field
Pablo Englebienne wrote: OK, I started over with the CHCl3 box from scratch. I prepared the following itp file from the CHCL3 parameters in ffG53a5.rtp: ---[chcl3.itp]--- [ moleculetype ] ; Namenrexcl CHCL3 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass 1 HCHL 1 CHCL3 HChL 1 0.082 1.008 2 CCHL 1 CHCL3 CChL 1 0.179 12.011 3 CLCHL 1 CHCL3 CLCh1 1 -0.087 35.453 4 CLCHL 1 CHCL3 CLCh2 1 -0.087 35.453 5 CLCHL 1 CHCL3 CLCh3 1 -0.087 35.453 [ bonds ] ; aiaj funct 1 2 2gb_39 2 3 2gb_40 2 4 2gb_40 2 5 2gb_40 1 3 2gb_47 1 4 2gb_47 1 5 2gb_47 3 4 2gb_48 3 5 2gb_48 4 5 2gb_48 [ angles ] ; aiajak funct 1 2 3 2 ga_43 1 2 4 2 ga_43 1 2 5 2 ga_43 3 2 4 2 ga_44 3 2 5 2 ga_44 4 2 5 2 ga_44 ---[chcl3.itp]--- I noticed that G53a5 includes 4 types of bond stretching terms specific for CHCl3 (C-Cl, C-H, H-Cl and Cl-Cl), therefore I specified all of them. Should all of these terms be harmonic bonds (function type 2) or some (e.g., the H-Cl and Cl-Cl terms) should be type 6 (as described in section 5.4 of the manual)? I tried with both types and I get the same minimized structure with the following topology and mdp files: The bonds defined correspond with what I get when I run pdb2gmx on a chloroform molecule, so I would suspect you have them properly defined as function type 2, although pdb2gmx defines many more angles and even dihedrals, probably given the weird bonding setup in CHCl3. I don't know how that might affect your system. I also discovered a minor bug in the Gromos96 .rtp files in the CHCl3 directive - no bond is defined between C and H. Will file a bugzilla. -Justin ---[topol.top]--- ; Include forcefield parameters #include "ffG53a5.itp" #include "chcl3.itp" [ system ] ; Name Chloroform [ molecules ] ; Compound#mols CHCL3 1 ---[topol.top]--- ---[em.mdp]--- integrator = cg nsteps = 5 ; ;Energy minimizing stuff ; emtol = 1e-5 emstep = 0.01 ; ;Electrostatics ; coulombtype = cut-off rcoulomb= 0 ns_type = simple nstlist = 0 rlist= 0 ; ;vdW ; rvdw= 0 ; ; PBC ; pbc= no ---[em.mdp]--- In the minimized structure, not all C-Cl distances are equivalent, although the minimization converges OK. Any comments? ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: Chloroform (CHCl3) solvent box for G53a5 force field
OK, I started over with the CHCl3 box from scratch. I prepared the following itp file from the CHCL3 parameters in ffG53a5.rtp: ---[chcl3.itp]--- [ moleculetype ] ; Namenrexcl CHCL3 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass 1 HCHL 1 CHCL3 HChL 1 0.082 1.008 2 CCHL 1 CHCL3 CChL 1 0.179 12.011 3 CLCHL 1 CHCL3 CLCh1 1 -0.087 35.453 4 CLCHL 1 CHCL3 CLCh2 1 -0.087 35.453 5 CLCHL 1 CHCL3 CLCh3 1 -0.087 35.453 [ bonds ] ; aiaj funct 1 2 2gb_39 2 3 2gb_40 2 4 2gb_40 2 5 2gb_40 1 3 2gb_47 1 4 2gb_47 1 5 2gb_47 3 4 2gb_48 3 5 2gb_48 4 5 2gb_48 [ angles ] ; aiajak funct 1 2 3 2 ga_43 1 2 4 2 ga_43 1 2 5 2 ga_43 3 2 4 2 ga_44 3 2 5 2 ga_44 4 2 5 2 ga_44 ---[chcl3.itp]--- I noticed that G53a5 includes 4 types of bond stretching terms specific for CHCl3 (C-Cl, C-H, H-Cl and Cl-Cl), therefore I specified all of them. Should all of these terms be harmonic bonds (function type 2) or some (e.g., the H-Cl and Cl-Cl terms) should be type 6 (as described in section 5.4 of the manual)? I tried with both types and I get the same minimized structure with the following topology and mdp files: ---[topol.top]--- ; Include forcefield parameters #include "ffG53a5.itp" #include "chcl3.itp" [ system ] ; Name Chloroform [ molecules ] ; Compound#mols CHCL3 1 ---[topol.top]--- ---[em.mdp]--- integrator = cg nsteps = 5 ; ; Energy minimizing stuff ; emtol = 1e-5 emstep = 0.01 ; ; Electrostatics ; coulombtype = cut-off rcoulomb= 0 ns_type = simple nstlist = 0 rlist = 0 ; ; vdW ; rvdw= 0 ; ; PBC ; pbc = no ---[em.mdp]--- In the minimized structure, not all C-Cl distances are equivalent, although the minimization converges OK. Any comments? ___ 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: Chloroform (CHCl3) solvent box for G53a5 force field
Pablo Englebienne wrote: Thanks for confirming this, Justin. I decided not to use the user-contributed CHCl3 box because the topology is not consistent with the GROMOS atom types: the CH is united atom (although the mass is 12.01100, it should probably be 13.01900?), while in G53a5 there are parameters for C, H and Cl. Has someone ever used this box successfully? I was able to equilibrate the box in NVT (100-200ps gives a stable simulation), although it exploded at constant pressure. After looking at some references on the mailing lists (both GMX and AMBER), I tried increasing tau_p from 2.0 to 5.0 and that yielded a stable 100 ps simulation, although the system later (continuing for further ~150 ps) started to oscillate wildly in temperature and pressure. What is the effect of increasing tau_p? Besides making the dynamics stable, would changing its value affect the outcome of the simulation in any other way? By increasing tau_p you are reducing the stringency of the pressure coupling, i.e. allowing the system to change a bit more between coordinate scaling. By decreasing the frequency of coordinate scaling in extremis, you would lose the benefit of pressure coupling and achieve an NVT ensemble, with the box dimensions being essentially static. In the case of a tau_p of 2.0 vs. 5.0, you should not have this problem. If the provided box uses a united-atom CH, I would suspect it is not suitable for GROMOS96 parameters, as you have discovered. In all G96 variants, the H is explicitly represented. You might consider coming up with your own box. Start with a coordinate file for one molecule, use genconf to generate a box, and equilibrate. If you want any further information about diagnosing the current problem, posting the .mdp file would be helpful. -Justin Thanks again! ___ 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 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: Chloroform (CHCl3) solvent box for G53a5 force field
I'm trying to simulate a small molecule in a chloroform box using the GROMOS G53a5 forcefield. I realized that the parameters for the solvent are present in the ffG53a5.rtp file, however I could not find a CHCl3 solvent box included in GROMACS. I did find, however, a CHCl3 solvent box equilibrated by PeiQuan Chen (http://lists.gromacs.org/pipermail/gmx-users/2003-May/005572.html) at http://www.gromacs.org/index.php?title=Download_%26_Installation/User_contributions/Molecule_topologies . I also saw mention of a box for the Amber forcefield, that is now included in AmberTools (amber10/dat/solvents/cform/cform.pdb and chcl3_equil.pdb.1). I took this one and I'm equilibrating it to use it later. In the mean time, I wanted to know if I overlooked something, and there is a CHCl3 box to use with the GROMOS forcefield? Not one that is officially distributed. If it was, it would be the /share/gromacs/top subdirectory with other solvent topologies and structures. Probably your best bet is to use the one in the User Contributions section, unless you feel the need to create your own and start from scratch. Thanks for confirming this, Justin. I decided not to use the user-contributed CHCl3 box because the topology is not consistent with the GROMOS atom types: the CH is united atom (although the mass is 12.01100, it should probably be 13.01900?), while in G53a5 there are parameters for C, H and Cl. Has someone ever used this box successfully? I was able to equilibrate the box in NVT (100-200ps gives a stable simulation), although it exploded at constant pressure. After looking at some references on the mailing lists (both GMX and AMBER), I tried increasing tau_p from 2.0 to 5.0 and that yielded a stable 100 ps simulation, although the system later (continuing for further ~150 ps) started to oscillate wildly in temperature and pressure. What is the effect of increasing tau_p? Besides making the dynamics stable, would changing its value affect the outcome of the simulation in any other way? Thanks again! ___ 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
