Re: [gmx-users] Parrinello-Rahman and Pairtype1 causing pressure instabilities
Hey y'all, Ran some additional simulations and, unfortunately, I'm still experiencing problems. Here's the mdp file that I used: integrator = md nsteps = 2000 ; 20 ns dt = 0.001000 nstlist = 20 ns_type = grid nstxout = 25000 nstvout = 25000 nstenergy = 25000 nstlog = 25000 continuation= yes constraints = none lincs_iter = 1 lincs_order = 4 cutoff-scheme = Verlet rcoulomb= 1.4 rvdw= 1.4 coulombtype = PME vdwtype = PME pme_order = 4 fourierspacing = 0.12 tcoupl = Nose-Hoover tc-grps = System tau_t = 0.10 ref_t = 300.00 nsttcouple = 5 pcoupl = Parrinello-Rahman pcoupltype = isotropic tau_p = 1.00 ref_p = 1.00 compressibility = 0.45 refcoord_scaling= com pbc = xyz periodic-molecules = no DispCorr= EnerPres gen_vel = no The simulation ran for 40ns with the Berendsen barostat just fine - density and volume were well-equilibrated within 1ns of the simulation starting. Unstable density fluctuations began immediately after switching to the PR barostat (from the output configuration of the previous 40ns run) and the simulation failed within 0.4ns. Here are some links to: - topology file: https://drive.google.com/open?id=1NF5EPbM2mnTGilXpOf7pQK5qlelBd8KC - initial configuration: https://drive.google.com/file/d/1kxMOKQcsAEheBCEAbkGcXqfBDwsHKpwr/view?usp=sharing - log file of second half of Berendsen run: https://drive.google.com/file/d/15TgbOOr6_fb8FkqR-nFHR8j1qbhTNT-Q/view?usp=sharing - log file of PR run: https://drive.google.com/file/d/1CPobb3ddDsd4I6Fce1tEpwHiBd5yq-tE/view?usp=sharing Thanks! If you need any other files or information, please let me know. -Wes On Tue, Mar 24, 2020 at 3:44 AM Justin Lemkul wrote: > > > On 3/24/20 3:09 AM, Wesley Michaels wrote: > > Hi, > > > > Thanks for your reply! I built the topology with my own script, as > opposed > > to using pdb2gmx. Following Bogdan's instructions here ( > > > https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2012-December/077005.html > ), > > I specified all instances of 1-4 pair interactions (i.e. pairs of atom > > indices) in the [ pairs ] section, but let GMX specify the [ pairtypes ] > > section (i.e. the interaction parameters for pairs of atom types) > > automatically using "gen_pairs" = "yes". > > > > As a second test, I generated a topology using pdb2gmx and the procedure > > Justin detailed here ( > > > https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2009-March/040125.html > ) > > (using the OPLS-AA FF option in pdb2gmx) and used that in a trial > > simulation. I experienced the same issue, unfortunately. Happy to provide > > any files as needed to help clarify the issue. > > If pdb2gmx built the topology and you're using an unaltered > forcefield.itp [defaults] directive, based on what you've said below, it > appears to just be an equilibration issue. Use Berendsen for a while to > get the system settled and then switch to Parrinello-Rahman. If you're > still experiencing problems, full .mdp file(s) would be helpful. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > == > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Parrinello-Rahman and Pairtype1 causing pressure instabilities
On 3/24/20 3:09 AM, Wesley Michaels wrote: Hi, Thanks for your reply! I built the topology with my own script, as opposed to using pdb2gmx. Following Bogdan's instructions here ( https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2012-December/077005.html), I specified all instances of 1-4 pair interactions (i.e. pairs of atom indices) in the [ pairs ] section, but let GMX specify the [ pairtypes ] section (i.e. the interaction parameters for pairs of atom types) automatically using "gen_pairs" = "yes". As a second test, I generated a topology using pdb2gmx and the procedure Justin detailed here ( https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2009-March/040125.html) (using the OPLS-AA FF option in pdb2gmx) and used that in a trial simulation. I experienced the same issue, unfortunately. Happy to provide any files as needed to help clarify the issue. If pdb2gmx built the topology and you're using an unaltered forcefield.itp [defaults] directive, based on what you've said below, it appears to just be an equilibration issue. Use Berendsen for a while to get the system settled and then switch to Parrinello-Rahman. If you're still experiencing problems, full .mdp file(s) would be helpful. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Parrinello-Rahman and Pairtype1 causing pressure instabilities
Hi,
Thanks for your reply! I built the topology with my own script, as opposed
to using pdb2gmx. Following Bogdan's instructions here (
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2012-December/077005.html),
I specified all instances of 1-4 pair interactions (i.e. pairs of atom
indices) in the [ pairs ] section, but let GMX specify the [ pairtypes ]
section (i.e. the interaction parameters for pairs of atom types)
automatically using "gen_pairs" = "yes".
As a second test, I generated a topology using pdb2gmx and the procedure
Justin detailed here (
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2009-March/040125.html)
(using the OPLS-AA FF option in pdb2gmx) and used that in a trial
simulation. I experienced the same issue, unfortunately. Happy to provide
any files as needed to help clarify the issue.
Thanks,
Wes
On Mon, Mar 23, 2020 at 3:54 AM Alessandra Villa <
alessandra.villa.bio...@gmail.com> wrote:
> Hi
>
> On Sat, Mar 21, 2020 at 3:20 AM Wesley Michaels
> wrote:
>
> > Hello,
> >
> > I hope this message finds you well! I'm running a pretty simple
> simulation
> > of a polyethylene melt (N = 100, 50 chains in the simulation, T = 500K,
> P =
> > 1atm, NPT ensemble, dt = 1 fs, OPLS-AA FF). My simulations are exhibiting
> > large, unstable volume fluctuations when I use the combination of the
> > Parrinello-Rahman barostat and pairtype = 1 for 1-4 pairs. I don't see
> this
> > behavior with {PR barostat and pairtype = 2} or {Berendsen barostat and
> > pairtype = 1}.
> >
> > I've specified the 1-4 pairs explicitly in the "[ pairs ]" section and
> set
> > "gen_pairs" to "yes" in the defaults section. I'm sure I'm missing
> > something obvious, but here are the troubleshooting steps I've tried:
> >
> >
> Sorry I could not understand the reason behind the modification you did.
> Standard OPLS-AA force field field has "gen_pairs" to "yes" in
> forcefield.itp and calculate the 1-4 interaction by uniformly scaling the
> parameters.
> No modifications are needed in the [pairs] section of the topol.top for
> standard simulations with OPLS-AA. Or do you want to do something else?
> See
>
> http://manual.gromacs.org/current/reference-manual/topologies/molecule-definition.html?highlight=pair
>
> to understand if your setting is inline which the force field.
>
> Best regards
>
> Alessandra
>
> > 1) ensure the simulation is equilibrated (up to 100 nanoseconds with
> > Berendsen barostat beforehand, which is more than plenty I believe);
> > 2) use a smaller time step (down to 0.01 fs);
> > 3) increase the pressure coupling time constant (up to 10 ps);
> > 4) using both GROMACS 2018 and GROMACS 2019.
> >
> > As far as energies go, I don't think there are worryingly large terms
> that
> > would blow the simulation up. Here's an example prepared with `gmx
> energy`:
> > Time (ps) Bond G96Angle RB LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Total
> > Energy Conserved En. Volume Density
> > 0 3.10E+04 5.40E+04 2.29E+04 8.76E+03 -1.66E+03 -4.71E+03 5.27E+03
> 2.17E+05
> > 2.17E+05 291.0 400.8
> > 2 5.11E+04 5.71E+04 8.24E+03 5.48E+02 -3.00E+03 -3.68E+03 9.01E+03
> 2.12E+05
> > 1.02E+06 3720.8 31.3
> > 4 2.56E+03 9.53E+03 8.18E+03 4.80E+03 -4.16E+03 -4.27E+03 9.40E+03
> 1.19E+05
> > 1.25E+06 21855.1 5.3
> > 6 4.76E+03 1.48E+04 1.15E+04 5.36E+03 -3.71E+03 -4.02E+03 8.68E+03
> 1.31E+05
> > 1.52E+06 88422.7 1.3
> > 8 6.58E+03 2.07E+04 1.48E+04 6.13E+03 -3.27E+03 -4.02E+03 7.95E+03
> 1.44E+05
> > 1.80E+06 246764.8 0.5
> > 10 1.05E+04 2.80E+04 1.64E+04 6.46E+03 -3.03E+03 -3.98E+03 7.61E+03
> > 1.57E+05
> > 2.08E+06 538599.2 0.2
> >
> >
> > Eventually, the volume becomes unphysically large and the density
> extremely
> > low. I'm sure I'm missing something obvious here (sorry for yet another
> "my
> > simulation is blowing up" question), so any insight into other steps I
> > could try would be greatly appreciated. If I can provide any additional
> > information (e.g. topology/mdp files), just let me know.
> >
> > Thanks,
> > Wes
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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Re: [gmx-users] Parrinello-Rahman and Pairtype1 causing pressure instabilities
Hi
On Sat, Mar 21, 2020 at 3:20 AM Wesley Michaels
wrote:
> Hello,
>
> I hope this message finds you well! I'm running a pretty simple simulation
> of a polyethylene melt (N = 100, 50 chains in the simulation, T = 500K, P =
> 1atm, NPT ensemble, dt = 1 fs, OPLS-AA FF). My simulations are exhibiting
> large, unstable volume fluctuations when I use the combination of the
> Parrinello-Rahman barostat and pairtype = 1 for 1-4 pairs. I don't see this
> behavior with {PR barostat and pairtype = 2} or {Berendsen barostat and
> pairtype = 1}.
>
> I've specified the 1-4 pairs explicitly in the "[ pairs ]" section and set
> "gen_pairs" to "yes" in the defaults section. I'm sure I'm missing
> something obvious, but here are the troubleshooting steps I've tried:
>
>
Sorry I could not understand the reason behind the modification you did.
Standard OPLS-AA force field field has "gen_pairs" to "yes" in
forcefield.itp and calculate the 1-4 interaction by uniformly scaling the
parameters.
No modifications are needed in the [pairs] section of the topol.top for
standard simulations with OPLS-AA. Or do you want to do something else?
See
http://manual.gromacs.org/current/reference-manual/topologies/molecule-definition.html?highlight=pair
to understand if your setting is inline which the force field.
Best regards
Alessandra
> 1) ensure the simulation is equilibrated (up to 100 nanoseconds with
> Berendsen barostat beforehand, which is more than plenty I believe);
> 2) use a smaller time step (down to 0.01 fs);
> 3) increase the pressure coupling time constant (up to 10 ps);
> 4) using both GROMACS 2018 and GROMACS 2019.
>
> As far as energies go, I don't think there are worryingly large terms that
> would blow the simulation up. Here's an example prepared with `gmx energy`:
> Time (ps) Bond G96Angle RB LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Total
> Energy Conserved En. Volume Density
> 0 3.10E+04 5.40E+04 2.29E+04 8.76E+03 -1.66E+03 -4.71E+03 5.27E+03 2.17E+05
> 2.17E+05 291.0 400.8
> 2 5.11E+04 5.71E+04 8.24E+03 5.48E+02 -3.00E+03 -3.68E+03 9.01E+03 2.12E+05
> 1.02E+06 3720.8 31.3
> 4 2.56E+03 9.53E+03 8.18E+03 4.80E+03 -4.16E+03 -4.27E+03 9.40E+03 1.19E+05
> 1.25E+06 21855.1 5.3
> 6 4.76E+03 1.48E+04 1.15E+04 5.36E+03 -3.71E+03 -4.02E+03 8.68E+03 1.31E+05
> 1.52E+06 88422.7 1.3
> 8 6.58E+03 2.07E+04 1.48E+04 6.13E+03 -3.27E+03 -4.02E+03 7.95E+03 1.44E+05
> 1.80E+06 246764.8 0.5
> 10 1.05E+04 2.80E+04 1.64E+04 6.46E+03 -3.03E+03 -3.98E+03 7.61E+03
> 1.57E+05
> 2.08E+06 538599.2 0.2
>
>
> Eventually, the volume becomes unphysically large and the density extremely
> low. I'm sure I'm missing something obvious here (sorry for yet another "my
> simulation is blowing up" question), so any insight into other steps I
> could try would be greatly appreciated. If I can provide any additional
> information (e.g. topology/mdp files), just let me know.
>
> Thanks,
> Wes
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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> send a mail to gmx-users-requ...@gromacs.org.
>
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[gmx-users] Parrinello-Rahman and Pairtype1 causing pressure instabilities
Hello,
I hope this message finds you well! I'm running a pretty simple simulation
of a polyethylene melt (N = 100, 50 chains in the simulation, T = 500K, P =
1atm, NPT ensemble, dt = 1 fs, OPLS-AA FF). My simulations are exhibiting
large, unstable volume fluctuations when I use the combination of the
Parrinello-Rahman barostat and pairtype = 1 for 1-4 pairs. I don't see this
behavior with {PR barostat and pairtype = 2} or {Berendsen barostat and
pairtype = 1}.
I've specified the 1-4 pairs explicitly in the "[ pairs ]" section and set
"gen_pairs" to "yes" in the defaults section. I'm sure I'm missing
something obvious, but here are the troubleshooting steps I've tried:
1) ensure the simulation is equilibrated (up to 100 nanoseconds with
Berendsen barostat beforehand, which is more than plenty I believe);
2) use a smaller time step (down to 0.01 fs);
3) increase the pressure coupling time constant (up to 10 ps);
4) using both GROMACS 2018 and GROMACS 2019.
As far as energies go, I don't think there are worryingly large terms that
would blow the simulation up. Here's an example prepared with `gmx energy`:
Time (ps) Bond G96Angle RB LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Total
Energy Conserved En. Volume Density
0 3.10E+04 5.40E+04 2.29E+04 8.76E+03 -1.66E+03 -4.71E+03 5.27E+03 2.17E+05
2.17E+05 291.0 400.8
2 5.11E+04 5.71E+04 8.24E+03 5.48E+02 -3.00E+03 -3.68E+03 9.01E+03 2.12E+05
1.02E+06 3720.8 31.3
4 2.56E+03 9.53E+03 8.18E+03 4.80E+03 -4.16E+03 -4.27E+03 9.40E+03 1.19E+05
1.25E+06 21855.1 5.3
6 4.76E+03 1.48E+04 1.15E+04 5.36E+03 -3.71E+03 -4.02E+03 8.68E+03 1.31E+05
1.52E+06 88422.7 1.3
8 6.58E+03 2.07E+04 1.48E+04 6.13E+03 -3.27E+03 -4.02E+03 7.95E+03 1.44E+05
1.80E+06 246764.8 0.5
10 1.05E+04 2.80E+04 1.64E+04 6.46E+03 -3.03E+03 -3.98E+03 7.61E+03 1.57E+05
2.08E+06 538599.2 0.2
Eventually, the volume becomes unphysically large and the density extremely
low. I'm sure I'm missing something obvious here (sorry for yet another "my
simulation is blowing up" question), so any insight into other steps I
could try would be greatly appreciated. If I can provide any additional
information (e.g. topology/mdp files), just let me know.
Thanks,
Wes
--
Gromacs Users mailing list
* Please search the archive at
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