On September 9, 2010 at 10:04 PM "Justin A. Lemkul" <jalem...@vt.edu> wrote:
>
>
> TJ Mustard wrote:
>
> <snip>
>
> > *Positional restraint mdp file:*
> >
> >
> >
> > define = -DPOSRES
> > constraints = all-bonds
> > integrator = md
> > dt = 0.004 ; ps
>
> Unless you're using virtual sites (which, per your commands below, you are not)
> this time step is inappropriately large and is a likely source of instability.
> With plain constraints, 2 fs is more appropriate.
>
>
> TJ Mustard wrote:
>
> <snip>
>
> > *Positional restraint mdp file:*
> >
> >
> >
> > define = -DPOSRES
> > constraints = all-bonds
> > integrator = md
> > dt = 0.004 ; ps
>
> Unless you're using virtual sites (which, per your commands below, you are not)
> this time step is inappropriately large and is a likely source of instability.
> With plain constraints, 2 fs is more appropriate.
Yes I usually run at 2 fs. I was actually running a huge batch of these at varying time steps and with or without -heavyh.
> > > nsteps = 2500 ; total ps = dt*nsteps
> > nstcomm = 1
> > nstxout = 200 ; output coordinates every ps = dt*nstxout
> > nstvout = 1000 ; output velocities every ps = dt*nstvout
> > nstfout = 0
> > nstenergy = 10
> > nstlog = 10
> > nstlist = 10
> > ns_type = grid
> > rlist = 0.9
> > coulombtype = PME
> > rcoulomb = 0.9
> > rvdw = 1.0
> > 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
> > Tcoupl = v-rescale
> > tau_t = 0.1 0.1 0.1 0.1 0.1
> > tc_grps = protein RNA SOL NA CL
>
> Also a major concern - never couple solvent and ions separately! See here:
>
> http://www.gromacs.org/Documentation/Terminology/Thermostats
>
> > nstcomm = 1
> > nstxout = 200 ; output coordinates every ps = dt*nstxout
> > nstvout = 1000 ; output velocities every ps = dt*nstvout
> > nstfout = 0
> > nstenergy = 10
> > nstlog = 10
> > nstlist = 10
> > ns_type = grid
> > rlist = 0.9
> > coulombtype = PME
> > rcoulomb = 0.9
> > rvdw = 1.0
> > 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
> > Tcoupl = v-rescale
> > tau_t = 0.1 0.1 0.1 0.1 0.1
> > tc_grps = protein RNA SOL NA CL
>
> Also a major concern - never couple solvent and ions separately! See here:
>
> http://www.gromacs.org/Documentation/Terminology/Thermostats
>
Yes I have since switched to a Protein Non-protein setting.
> > ref_t = 310 310 310 310 310
> > ; Pressure coupling is on
> > pcoupl = berendsen
> > pcoupltype = isotropic
> > tau_p = 0.5
> > compressibility = 4.5e-5
> > ref_p = 1.0
> > ; Generate velocities is on at 310K (core body temp)
> > gen_vel = yes
> > gen_temp = 310.0
> > gen_seed = 173529
> >
> >
> >
> >
> >
> > *main molecular dynamics mdp file:*
> >
> >
> >
>
> <snip>
>
> > define = -DPOSRES
>
> > ; Pressure coupling is on
> > pcoupl = berendsen
> > pcoupltype = isotropic
> > tau_p = 0.5
> > compressibility = 4.5e-5
> > ref_p = 1.0
> > ; Generate velocities is on at 310K (core body temp)
> > gen_vel = yes
> > gen_temp = 310.0
> > gen_seed = 173529
> >
> >
> >
> >
> >
> > *main molecular dynamics mdp file:*
> >
> >
> >
>
> <snip>
>
> > define = -DPOSRES
>
> Restraints during data collection, or did you paste the wrong file?
Yeah that will be fixed asap.
> > <snip>
>
> > ; Generate velocities is on at 310K (core body temp)
> > gen_vel = yes
>
> Re-generating velocities after equilibration defeats the whole purpose of
> equilibrating. Per your commands below, you are not preserving the velocities
> (grompp -t with .trr or .cpt file) obtained during your PR equilibration.
>
>
> > ; Generate velocities is on at 310K (core body temp)
> > gen_vel = yes
>
> Re-generating velocities after equilibration defeats the whole purpose of
> equilibrating. Per your commands below, you are not preserving the velocities
> (grompp -t with .trr or .cpt file) obtained during your PR equilibration.
>
Yeah that will be fixed asap.
> > gen_temp = 310.0
> > gen_seed = 173529
> >
> >
> >
> >
> >
> > *And my script for running the whole process:*
> >
> >
> >
> > pdb2gmx -f receptor.pdb -o receptor.gro -p receptor.top
> >
> > editconf -bt cubic -f receptor.gro -o receptor.gro -c -d 1.5
> >
> > genbox -cp receptor.gro -cs spc216.gro -o receptor_b4ion.gro -p receptor.top
> >
> > grompp -f em.mdp -c receptor_b4ion.gro -p receptor.top -o receptor_b4ion.tpr
> >
> > genion -s receptor_b4ion.tpr -o receptor_b4em.gro -neutral -conc 0.0001
> > -pname NA -nname CL -g receptor_ion.log -p receptor.top
> >
> >
> >
> > *Here I select the SOL for ions...*
> >
> >
> >
> > grompp -f em.mdp -c receptor_b4em.gro -p receptor.top -o receptor_em.tpr
> >
> > mdrun -v -s receptor_em.tpr -c "$base"_after_em.gro -g emlog.log
> >
> > grompp -f pr.mdp -c receptor_after_em.gro -p receptor.top -o receptor_pr.tpr
> >
> > mdrun -v -s receptor_pr.tpr -o receptor_pr.trr -e pr.edr -c
> > receptor_after_pr.gro -g prlog.log -cpi state_pr.cpt -cpo state_pr.cpt
> >
> > grompp -f md.mdp -c receptor_after_pr.gro -p receptor.top -o receptor_md.tpr
> >
> > mdrun -s receptor_md.tpr -o receptor_md.trr -c receptor_after_pr.gro -g
> > md.log -e md.edr -cpi state_md.cpt -cpo state_md.cpt
> >
> > *Where receptor is of course my protein/RNA pdb name*
> >
> >
> >
> > I always make sure that the pdb doesn't give me notes or warnings or
> > errors of course in the pdb2gmx step. Most of the time I minimize to my
> > computers "machine precision."
> >
> > **
> >
> > *This is the return I get from the "EM" step:*
> >
> >
> >
> > Stepsize too small, or no change in energy.
> > Converged to machine precision,
> > but not to the requested precision Fmax < 200
> >
> > Double precision normally gives you higher accuracy.
> > You might need to increase your constraint accuracy, or turn
> > off constraints alltogether (set constraints = none in mdp file)
> >
> > writing lowest energy coordinates.
> >
> > Steepest Descents converged to machine precision in 324 steps,
> > but did not reach the requested Fmax < 200.
> > Potential Energy = -1.9868888e+07
> > Maximum force = 8.7276396e+03 on atom 19080
>
> This is a very high Fmax, indicating that you have bad clashes in your system
> that, when combined with the parameters above, surely leads to an unstable
> system. The fact that Gromos96 works is a bit curious, but you have too many
> potential pitfalls listed here to specifically diagnose the difference based on
> this information alone.
>
> -Justin
> > gen_seed = 173529
> >
> >
> >
> >
> >
> > *And my script for running the whole process:*
> >
> >
> >
> > pdb2gmx -f receptor.pdb -o receptor.gro -p receptor.top
> >
> > editconf -bt cubic -f receptor.gro -o receptor.gro -c -d 1.5
> >
> > genbox -cp receptor.gro -cs spc216.gro -o receptor_b4ion.gro -p receptor.top
> >
> > grompp -f em.mdp -c receptor_b4ion.gro -p receptor.top -o receptor_b4ion.tpr
> >
> > genion -s receptor_b4ion.tpr -o receptor_b4em.gro -neutral -conc 0.0001
> > -pname NA -nname CL -g receptor_ion.log -p receptor.top
> >
> >
> >
> > *Here I select the SOL for ions...*
> >
> >
> >
> > grompp -f em.mdp -c receptor_b4em.gro -p receptor.top -o receptor_em.tpr
> >
> > mdrun -v -s receptor_em.tpr -c "$base"_after_em.gro -g emlog.log
> >
> > grompp -f pr.mdp -c receptor_after_em.gro -p receptor.top -o receptor_pr.tpr
> >
> > mdrun -v -s receptor_pr.tpr -o receptor_pr.trr -e pr.edr -c
> > receptor_after_pr.gro -g prlog.log -cpi state_pr.cpt -cpo state_pr.cpt
> >
> > grompp -f md.mdp -c receptor_after_pr.gro -p receptor.top -o receptor_md.tpr
> >
> > mdrun -s receptor_md.tpr -o receptor_md.trr -c receptor_after_pr.gro -g
> > md.log -e md.edr -cpi state_md.cpt -cpo state_md.cpt
> >
> > *Where receptor is of course my protein/RNA pdb name*
> >
> >
> >
> > I always make sure that the pdb doesn't give me notes or warnings or
> > errors of course in the pdb2gmx step. Most of the time I minimize to my
> > computers "machine precision."
> >
> > **
> >
> > *This is the return I get from the "EM" step:*
> >
> >
> >
> > Stepsize too small, or no change in energy.
> > Converged to machine precision,
> > but not to the requested precision Fmax < 200
> >
> > Double precision normally gives you higher accuracy.
> > You might need to increase your constraint accuracy, or turn
> > off constraints alltogether (set constraints = none in mdp file)
> >
> > writing lowest energy coordinates.
> >
> > Steepest Descents converged to machine precision in 324 steps,
> > but did not reach the requested Fmax < 200.
> > Potential Energy = -1.9868888e+07
> > Maximum force = 8.7276396e+03 on atom 19080
>
> This is a very high Fmax, indicating that you have bad clashes in your system
> that, when combined with the parameters above, surely leads to an unstable
> system. The fact that Gromos96 works is a bit curious, but you have too many
> potential pitfalls listed here to specifically diagnose the difference based on
> this information alone.
>
> -Justin
Thank you. I will be making these changes and running the batch again very soon. If I hit the same issues I will post again.
> > > Norm of force = 3.8592850e+01
> >
> >
> >
> >
> >
> > *I will get this error sometime in the "PR" step of my script:*
> >
> >
> >
> > step 0
> > Step 11 Warning: pressure scaling more than 1%, mu: 1.03087 1.03087 1.03087
> >
> > Step 11 Warning: pressure scaling more than 1%, mu: 1.03087 1.03087 1.03087
> >
> > Step 21 Warning: pressure scaling more than 1%, mu: 0.849053 0.849053
> > 0.849053
> >
> > Step 21 Warning: pressure scaling more than 1%, mu: 0.849053 0.849053
> > 0.849053
> >
> > Step 22, time 0.088 (ps) LINCS WARNING
> > relative constraint deviation after LINCS:
> > rms 0.005723, max 0.026407 (between atoms 6545 and 6542)
> > bonds that rotated more than 30 degrees:
> > atom 1 atom 2 angle previous, current, constraint length
> >
> >
> >
> >
> >
> >
> >
> > I hope this is enough information. Any help would be much appreciated.
> >
> >
> >
> > TJ Mustard
> > Email: musta...@onid.orst.edu
> > Cell: 509-879-4173
> >
> > On September 9, 2010 at 9:11 PM "Justin A. Lemkul" <jalem...@vt.edu> wrote:
> >
> > >
> > >
> > > TJ Mustard wrote:
> > > >
> > > > First off I am using gromacs 4.5. I will also post all of my files and
> > > > errors if they help.
> > > >
> > > >
> > > >
> > > > If I run a protein in GROMOS96 all my md runs complete succesfully. But
> > > > if I change to any of the AMBER force fields I get LINCS errors in my
> > > > positional restraint md run. I have tried using shake, 1 fs step sizes,
> > > > -heavyh, and many more. Does anyone know what is going on here?
> > > >
> > >
> > > A complete (but not overly lengthy) post will save everyone a lot of
> > time.
> > > Based on the information you've provided here, I see now way to
> > diagnose the
> > > problem. The most important information to post would be your .mdp file.
> > > Certain settings can influence stability. A description of the hardware,
> > > compilers used, etc. can also be useful.
> > >
> > > -Justin
> > >
> > > >
> > > >
> > > > The reason I want to use AMBER is the fact that I want to run md on the
> > > > 30s rybosome and amber converts RNA much easier than GROMOS force
> > fields.
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > Thank you in advance,
> > > >
> > > >
> > > >
> > > > TJ Mustard Email: musta...@onid.orst.edu
> > > > Cell: 509-879-4173
> > > >
> > > >
> > > >
> > > >
> > >
> > > --
> > > ========================================
> > >
> > > 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
> > >
> >
> >
> >
> >
> >
>
> --
> ========================================
>
> 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
>
> >
> >
> >
> >
> >
> > *I will get this error sometime in the "PR" step of my script:*
> >
> >
> >
> > step 0
> > Step 11 Warning: pressure scaling more than 1%, mu: 1.03087 1.03087 1.03087
> >
> > Step 11 Warning: pressure scaling more than 1%, mu: 1.03087 1.03087 1.03087
> >
> > Step 21 Warning: pressure scaling more than 1%, mu: 0.849053 0.849053
> > 0.849053
> >
> > Step 21 Warning: pressure scaling more than 1%, mu: 0.849053 0.849053
> > 0.849053
> >
> > Step 22, time 0.088 (ps) LINCS WARNING
> > relative constraint deviation after LINCS:
> > rms 0.005723, max 0.026407 (between atoms 6545 and 6542)
> > bonds that rotated more than 30 degrees:
> > atom 1 atom 2 angle previous, current, constraint length
> >
> >
> >
> >
> >
> >
> >
> > I hope this is enough information. Any help would be much appreciated.
> >
> >
> >
> > TJ Mustard
> > Email: musta...@onid.orst.edu
> > Cell: 509-879-4173
> >
> > On September 9, 2010 at 9:11 PM "Justin A. Lemkul" <jalem...@vt.edu> wrote:
> >
> > >
> > >
> > > TJ Mustard wrote:
> > > >
> > > > First off I am using gromacs 4.5. I will also post all of my files and
> > > > errors if they help.
> > > >
> > > >
> > > >
> > > > If I run a protein in GROMOS96 all my md runs complete succesfully. But
> > > > if I change to any of the AMBER force fields I get LINCS errors in my
> > > > positional restraint md run. I have tried using shake, 1 fs step sizes,
> > > > -heavyh, and many more. Does anyone know what is going on here?
> > > >
> > >
> > > A complete (but not overly lengthy) post will save everyone a lot of
> > time.
> > > Based on the information you've provided here, I see now way to
> > diagnose the
> > > problem. The most important information to post would be your .mdp file.
> > > Certain settings can influence stability. A description of the hardware,
> > > compilers used, etc. can also be useful.
> > >
> > > -Justin
> > >
> > > >
> > > >
> > > > The reason I want to use AMBER is the fact that I want to run md on the
> > > > 30s rybosome and amber converts RNA much easier than GROMOS force
> > fields.
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > Thank you in advance,
> > > >
> > > >
> > > >
> > > > TJ Mustard Email: musta...@onid.orst.edu
> > > > Cell: 509-879-4173
> > > >
> > > >
> > > >
> > > >
> > >
> > > --
> > > ========================================
> > >
> > > 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
> > >
> >
> >
> >
> >
> >
>
> --
> ========================================
>
> 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
>
TJ Mustard
Email: musta...@onid.orst.edu
-- 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
