Re: [gmx-users] Water molecule starting at atom X can not be settled; can't find a solution
Hi Simone, The temperature coupling might be a cause for an error like that to occur. Try to understand that coupling ions separately may cause large fluctuations in there velocities and hence cause sudden large displacements that may put an ion on top of a solvent molecule that can't be settled anymore due to that. I assume you fixed that error, but think it's good to have a bit of background (and please read some more) to help avoiding such mistakes later on. If the problem persists while the T-coupling error is fixed, then there's something else wrong :) Is it always the same water molecule, or are they always in the neighbourhood, or does the error occur at random water molecules? Is the water molecule close to the edge of the box when the error occurs? Since you have all frames, you can easily check the trajectory all the way :) You may also try running with NVT to see whether that fixes the problem. Did you actually equilibrate the temperature first, before putting the pressure on? O, and you might want to show your md.mdp, as that's where the simulation is breaking. Hope it helps, Tsjerk On Fri, Oct 16, 2009 at 1:49 PM, Justin A. Lemkul wrote: > > > Simone Cirri wrote: >> >> Justin A. Lemkul wrote: >> >> ; Berendsen temperature coupling is on in three groups >> Tcoupl = berendsen >> >> tau_t = 0.1 0.1 0.1 tc-grps = protein sol NA+ >> >> ref_t = 300 300 300 >> >> Never couple solvent and ions separately. Surely grompp warned you >> that you should be using "Protein Non-Protein"? See here: >> >> http://www.gromacs.org/Documentation/Terminology/Thermostats >> >> >> Hi Justin, thanks for the suggestion. Actually, it's an error I've always >> been doing and I'm glad I've solved it. >> However, I'm afraid it has nothing to do with the problem, because I just >> tried to run the MD again (after modifying the md.mdp as you told me) and >> the fatal error is still there. >> I've noticed the the T-coupling mistake is also in pr.mdp. Do you think >> that correcting it and re-running the PR simulation would fix the "water >> molecule can not be settled" problem? > > It's probably worth a shot. It's not appropriate to couple solvent and ions > separately in any phase, equilibration or data collection. > > -Justin > >> Anyway here is the pr.mdp (as it was before): >> >> title = hsacyx >> warnings = 10 >> cpp = /lib/cpp >> define = -DPOSRES >> constraints = all-bonds >> integrator = md >> dt = 0.002 ; ps ! >> nsteps = 10 ; total 200.0 ps. >> nstcomm = 1 >> nstxout = 250 >> nstvout = 1000 >> nstfout = 0 >> nstlog = 10 >> nstenergy = 10 >> nstlist = 10 >> ns_type = grid >> rlist = 0.9 >> coulombtype = PME >> rcoulomb = 0.9 >> rvdw = 0.9 >> fourierspacing = 0.12 >> fourier_nx = 0 >> fourier_ny = 0 >> fourier_nz = 0 >> pme_order = 6 >> ewald_rtol = 1e-5 >> optimize_fft = yes >> ; Berendsen temperature coupling is on in four groups >> Tcoupl = berendsen >> tau_t = 0.1 0.1 0.1 >> tc-grps = Protein SOL NA+ >> ref_t = 300 300 300 >> ; Pressure coupling is on >> Pcoupl = berendsen >> pcoupltype = isotropic >> tau_p = 0.5 >> compressibility = 4.5e-5 >> ref_p = 1.0 >> ; Generate velocites is on at 300 K. >> gen_vel = yes >> gen_temp = 300.0 >> gen_seed = 173529 >> >> Thank you >> >> Simone Cirri >> >> >> >> >> ___ >> gmx-users mailing list gmx-us...@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 list gmx-us...@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'
Re: [gmx-users] Water molecule starting at atom X can not be settled; can't find a solution
Simone Cirri wrote: Justin A. Lemkul wrote: ; Berendsen temperature coupling is on in three groups Tcoupl = berendsen tau_t = 0.1 0.1 0.1 tc-grps = protein sol NA+ ref_t = 300 300 300 Never couple solvent and ions separately. Surely grompp warned you that you should be using "Protein Non-Protein"? See here: http://www.gromacs.org/Documentation/Terminology/Thermostats Hi Justin, thanks for the suggestion. Actually, it's an error I've always been doing and I'm glad I've solved it. However, I'm afraid it has nothing to do with the problem, because I just tried to run the MD again (after modifying the md.mdp as you told me) and the fatal error is still there. I've noticed the the T-coupling mistake is also in pr.mdp. Do you think that correcting it and re-running the PR simulation would fix the "water molecule can not be settled" problem? It's probably worth a shot. It's not appropriate to couple solvent and ions separately in any phase, equilibration or data collection. -Justin Anyway here is the pr.mdp (as it was before): title = hsacyx warnings= 10 cpp = /lib/cpp define = -DPOSRES constraints = all-bonds integrator = md dt = 0.002; ps ! nsteps = 10; total 200.0 ps. nstcomm = 1 nstxout = 250 nstvout = 1000 nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = grid rlist = 0.9 coulombtype= PME rcoulomb= 0.9 rvdw= 0.9 fourierspacing= 0.12 fourier_nx= 0 fourier_ny= 0 fourier_nz= 0 pme_order= 6 ewald_rtol= 1e-5 optimize_fft= yes ; Berendsen temperature coupling is on in four groups Tcoupl = berendsen tau_t = 0.1 0.10.1 tc-grps= Protein SOLNA+ ref_t = 300 300300 ; Pressure coupling is on Pcoupl = berendsen pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp= 300.0 gen_seed= 173529 Thank you Simone Cirri ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Water molecule starting at atom X can not be settled; can't find a solution
Justin A. Lemkul wrote: ; Berendsen temperature coupling is on in three groups > Tcoupl = berendsen > > tau_t = 0.1 0.1 0.1 tc-grps = protein sol NA+ > > ref_t = 300 300 300 > > Never couple solvent and ions separately. Surely grompp warned you that you > should be using "Protein Non-Protein"? See here: > > http://www.gromacs.org/Documentation/Terminology/Thermostats > > Hi Justin, thanks for the suggestion. Actually, it's an error I've always been doing and I'm glad I've solved it. However, I'm afraid it has nothing to do with the problem, because I just tried to run the MD again (after modifying the md.mdp as you told me) and the fatal error is still there. I've noticed the the T-coupling mistake is also in pr.mdp. Do you think that correcting it and re-running the PR simulation would fix the "water molecule can not be settled" problem? Anyway here is the pr.mdp (as it was before): title = hsacyx warnings= 10 cpp = /lib/cpp define = -DPOSRES constraints = all-bonds integrator = md dt = 0.002; ps ! nsteps = 10; total 200.0 ps. nstcomm = 1 nstxout = 250 nstvout = 1000 nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = grid rlist = 0.9 coulombtype= PME rcoulomb= 0.9 rvdw= 0.9 fourierspacing= 0.12 fourier_nx= 0 fourier_ny= 0 fourier_nz= 0 pme_order= 6 ewald_rtol= 1e-5 optimize_fft= yes ; Berendsen temperature coupling is on in four groups Tcoupl = berendsen tau_t = 0.1 0.10.1 tc-grps= Protein SOLNA+ ref_t = 300 300300 ; Pressure coupling is on Pcoupl = berendsen pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp= 300.0 gen_seed= 173529 Thank you Simone Cirri ___ 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] Water molecule starting at atom X can not be settled; can't find a solution
Simone Cirri wrote: ; Berendsen temperature coupling is on in three groups Tcoupl = berendsen tau_t = 0.1 0.1 0.1 tc-grps= protein sol NA+ ref_t = 300 300 300 Never couple solvent and ions separately. Surely grompp warned you that you should be using "Protein Non-Protein"? See here: http://www.gromacs.org/Documentation/Terminology/Thermostats -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Water molecule starting at atom X can not be settled; can't find a solution
Hi everyone, in the last weeks I've been trying to run a simulation with Gromacs 4.0.5 and the force field ffamber99. The protein is albumine (BSA, bovine serum albumine), so it's a very big one (570+ residues). The solvent is tip3p. After an energy minimization run and a position restraint run, I start with the "real" simulation. Invariably, it crashes after 1 ps with the error message: t = 1.000 ps: Water molecule starting at atom 42031 can not be settled. Check for bad contacts and/or reduce the timestep. I've searched in the mailing list and I've tried many of the solutions you proposed: - I looked at the water molecule with the problematic atom to see if it was interacting in some weird way with the protein (I put ntsxout = 1 in order to have many more frames); but it isn't so, since that molecule is only one of the many solvent molecules that (at least in the first ps) stay far from the protein - I tried to run a longer and stronger minimization: so I increased the number of steps (from 1 to 2) and I decreased emtol (from 100 to 1), but nothing changed - I tried to increase the box dimensions; in editconf I put -c 1.2 (instead of 0.7), but nothing changed. - I checked the stepXXXb.pdb and stepXXXc.pdb that mdrun created after the crash, but I didn't see anything strange in them. - I did a longer position restraint run (3 ns instead of the usual 200 ps) but nothing changed... I was hoping that it would stabilize the water, but I think the problem is not that. Even though the energy minimization doesn't show any problems, I think that's the crucial part; as someone said in another message, the problem doesn't really involve the water molecule that cannot be settled, but other atoms in the protein with big forces that in some way collide with the water molecule... am I right? In this case, deleting the problematic water molecule could help? I thought it would be useless, since that molecule is not close to the protein at all... Here you have the em.mdp and the md.mdp, if you want I can also paste the pr.mdp . title = hsacyx cpp = /lib/cpp define = -DFLEX_SPC constraints = none integrator = steep dt = 0.002; ps ! nsteps = 2 nstlist = 10 ns_type = grid rlist = 0.9 coulombtype= PME rcoulomb= 0.9 rvdw= 0.9 fourierspacing= 0.12 fourier_nx= 0 fourier_ny= 0 fourier_nz= 0 pme_order= 6 ewald_rtol= 1e-5 optimize_fft= yes ; ; Energy minimizing stuff ; emtol = 1 emstep = 0.01 title = hsacyx cpp = /lib/cpp constraints = all-bonds integrator = md dt = 0.002; ps ! nsteps = 750; total 15000 ps. nstcomm = 1 nstxout = 2500 nstvout = 0 nstfout = 0 nstlist = 500 ns_type = grid rlist = 0.9 coulombtype= PME rcoulomb= 0.9 rvdw= 0.9 fourierspacing= 0.12 fourier_nx= 0 fourier_ny= 0 fourier_nz= 0 pme_order= 6 ewald_rtol= 1e-5 optimize_fft= yes ; Berendsen temperature coupling is on in three groups Tcoupl = berendsen tau_t = 0.1 0.1 0.1 tc-grps= protein sol NA+ ref_t = 300 300 300 ; Pressure coupling is on Pcoupl = berendsen pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp= 300.0 gen_seed= 173529 I really don't know what else I could do... if someone has an idea, I would be glad to hear it. Thank you Simone Cirri PhD student at the Structural Biology Lab of University of Siena, Italy ___ 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
