[gmx-users] No default bond types

[Neena Susan Eappen]

Hello gromacs users,

I just modified opls force field for a modified aminoacid with 4 new bond types 
and 9 new angle types. However, the command grompp gave a no default error for 
one bond and 6 angle types. Is there a way to resolve this?

Many thanks and Take care,
Neena

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[gmx-users] topology of co2

[Afsane Farhadi]

hi allI want to download a topology of co2  by opls as forcefield,  but many 
servers doesn't answer(like ligpargen and tppmktop). how can I find a topology 
for this molecule?

Sent from Yahoo Mail on Android
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[gmx-users] Drude polarization, practical matters

[Nicolás Marcelo Rozas Castro]

Hi everyone,
I'll be straight, my questions are:

1. It is possible to use Drude model in GROMACS 5.1.5?
2. How exactly this is done? If someone had an input file example (pdb
and/or itp) and can share it i'll appreciate.

Thank a lot!!

Nicolas Rozas Castro
Universidad de Chile
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Re: [gmx-users] Various questions related to Gromacs performance tuning

[Mark Abraham]

Hi,

There could certainly be a bug with -ddorder pp_pme, as there's no testing
done of that. If you can reproduce with a recent version of GROMACS, please
do file a bug report. (Though this week we're moving to new infrastructure,
so leave it for a day or two before trying to report it!

Mark

On Tue, 24 Mar 2020 at 21:03, Kutzner, Carsten  wrote:

> Hi,
>
> > Am 24.03.2020 um 16:28 schrieb Tobias Klöffel :
> >
> > Dear all,
> > I am very new to Gromacs so maybe some of my problems are very easy to
> fix:)
> > Currently I am trying to compile and benchmark gromacs on AMD rome cpus,
> the benchmarks are taken from:
> > https://www.mpibpc.mpg.de/grubmueller/bench
> >
> > 1) OpenMP parallelization: Is it done via OpenMP tasks?
> Yes, all over the code loops are parallelized via OpenMP via #pragma omp
> parallel for
> and similar directives.
>
> > If the Intel toolchain is detected and  -DGMX_FFT_LIBRARY=mkl is
> set,-mkl=serial is used, even though -DGMX_OPENMP=on is set.
> GROMACS uses only the serial transposes - allowing mkl to open up its own
> OpenMP threads
> would lead to oversubscription of cores and performance degradation.
>
> > 2) I am trying to use gmx_mpi tune_pme but I never got it to run. I do
> not really understand what I have to specify for -mdrun. I
> Normally you need a serial (read: non-mpi enabled) 'gmx' so that you can
> call
> gmx tune_pme. Most queueing systems don't like it if one parallel program
> calls
> another parallel program.
>
> > tried -mdrun 'gmx_mpi mdrun' and export MPIRUN="mpirun
> -use-hwthread-cpus -np $tmpi -map-by ppr:$tnode:node:pe=$OMP_NUM_THREADS
> --report-bindings" But it just complains that mdrun is not working.
> There should be an output somewhere with the exact command line that
> tune_pme invoked to test whether mdrun works. That should shed some light
> on the issue.
>
> Side note: Tuning is normally only useful on CPU-nodes. If your nodes also
> have GPUs, you will probably not want to do this kind of PME tuning.
>
> > Normal  execution via $MPIRUN gmx_mpi mdrun -s ... works
> >
> >
> > 3) As far as I understood, most time of PME is spent in a 3d FFT and
> hence probably most time is spent in a mpi alltoall communication.
> Yes, but that also depends a lot on the number of nodes you are running on.
> Check for yourself: Do a 'normal' mdrun (without tune_pme) on the number
> of
> nodes that you are interested and check the detailed timings at the end of
> the log file. There you will find how much time is spent in various PME
> routines.
>
> Best,
>   Carsten
>
> > For that reason I would like to place all PME tasks on a separate node
> via -ddorder pp_pme. If I do so, the calculations just hangs. Specifying
> -ddorder interleave or cartesian works without problems. Is this a known
> issue?
> >
> > Kind regards,
> > Tobias Klöffel
> >
> > --
> > M.Sc. Tobias Klöffel
> > ===
> > HPC (High Performance Computing) group
> > Erlangen Regional Computing Center(RRZE)
> > Friedrich-Alexander-Universität Erlangen-Nürnberg
> > Martensstr. 1
> > 91058 Erlangen
> >
> > Room: 1.133
> > Phone: +49 (0) 9131 / 85 - 20101
> >
> > ===
> >
> > E-mail: tobias.kloef...@fau.de
> >
> > --
> > 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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> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
> --
> Dr. Carsten Kutzner
> Max Planck Institute for Biophysical Chemistry
> Theoretical and Computational Biophysics
> Am Fassberg 11, 37077 Goettingen, Germany
> Tel. +49-551-2012313, Fax: +49-551-2012302
> http://www.mpibpc.mpg.de/grubmueller/kutzner
> http://www.mpibpc.mpg.de/grubmueller/sppexa
>
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Re: [gmx-users] Various questions related to Gromacs performance tuning

[Kutzner, Carsten]

Hi,

> Am 24.03.2020 um 16:28 schrieb Tobias Klöffel :
> 
> Dear all,
> I am very new to Gromacs so maybe some of my problems are very easy to fix:)
> Currently I am trying to compile and benchmark gromacs on AMD rome cpus, the 
> benchmarks are taken from:
> https://www.mpibpc.mpg.de/grubmueller/bench
> 
> 1) OpenMP parallelization: Is it done via OpenMP tasks?
Yes, all over the code loops are parallelized via OpenMP via #pragma omp 
parallel for
and similar directives.

> If the Intel toolchain is detected and  -DGMX_FFT_LIBRARY=mkl is 
> set,-mkl=serial is used, even though -DGMX_OPENMP=on is set.
GROMACS uses only the serial transposes - allowing mkl to open up its own 
OpenMP threads
would lead to oversubscription of cores and performance degradation.

> 2) I am trying to use gmx_mpi tune_pme but I never got it to run. I do not 
> really understand what I have to specify for -mdrun. I 
Normally you need a serial (read: non-mpi enabled) 'gmx' so that you can call
gmx tune_pme. Most queueing systems don't like it if one parallel program calls
another parallel program.

> tried -mdrun 'gmx_mpi mdrun' and export MPIRUN="mpirun -use-hwthread-cpus -np 
> $tmpi -map-by ppr:$tnode:node:pe=$OMP_NUM_THREADS --report-bindings" But it 
> just complains that mdrun is not working.
There should be an output somewhere with the exact command line that
tune_pme invoked to test whether mdrun works. That should shed some light
on the issue.

Side note: Tuning is normally only useful on CPU-nodes. If your nodes also
have GPUs, you will probably not want to do this kind of PME tuning.

> Normal  execution via $MPIRUN gmx_mpi mdrun -s ... works
> 
> 
> 3) As far as I understood, most time of PME is spent in a 3d FFT and hence 
> probably most time is spent in a mpi alltoall communication.
Yes, but that also depends a lot on the number of nodes you are running on.
Check for yourself: Do a 'normal' mdrun (without tune_pme) on the number of 
nodes that you are interested and check the detailed timings at the end of
the log file. There you will find how much time is spent in various PME
routines.

Best,
  Carsten

> For that reason I would like to place all PME tasks on a separate node via 
> -ddorder pp_pme. If I do so, the calculations just hangs. Specifying -ddorder 
> interleave or cartesian works without problems. Is this a known issue?
> 
> Kind regards,
> Tobias Klöffel
> 
> -- 
> M.Sc. Tobias Klöffel
> ===
> HPC (High Performance Computing) group
> Erlangen Regional Computing Center(RRZE)
> Friedrich-Alexander-Universität Erlangen-Nürnberg
> Martensstr. 1
> 91058 Erlangen
> 
> Room: 1.133
> Phone: +49 (0) 9131 / 85 - 20101
> 
> ===
> 
> E-mail: tobias.kloef...@fau.de
> 
> -- 
> 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.

--
Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302
http://www.mpibpc.mpg.de/grubmueller/kutzner
http://www.mpibpc.mpg.de/grubmueller/sppexa

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Re: [gmx-users] Conversion of improper angles from amber object file to gromacs

[Justin Lemkul]

On 3/24/20 3:26 PM, Daniel Bauer wrote:

Hi,

I  am trying to convert forcefield parameters of zwitterionic glycine
from an amber object file format to gromacs .rtp (to use it with
amber99sb, which lacks zwitterionic amino acids).

The amber library file I plan to use can be found here:
https://personalpages.manchester.ac.uk/staff/Richard.Bryce/amber/pro/zaa.off

This is what i have so far:

[ZG]
  [ atoms ]
  N    N3  -0.408600 1
     H1    H    0.300300 2
     H2    H    0.300300 3
     H3    H    0.300300 4
     CA    CT  -0.026400 5
    HA1    H1   0.073800 6
    HA2    H1   0.073800 7
  C    C    0.835500 8
  O    O2  -0.724500 9
    OXT    O2  -0.724500    10
  [ bonds ]
  N    H1
  N    H2
  N    H3
  N    CA
     CA   HA1
     CA   HA2
     CA C
  C O
  C    OXT

However, I am unsure about the correct conversion of impropers. In the
.off file format, those are based on the atom type, while gromacs
expects them to be based on atom names. This leaves room for some
ambiguity when the same atom type is used multiple types (i.e the COO or
NH3 group).

The improper parameter section of the .off file looks like this:

!entry.zaa_improper.parm.torsions table  str type1  str type2  str
type3  str type4  int type  dbl kp  int n  dbl p0  str desc
  "CT" "O2" "C" "O2" 1 10.50 2 3.141594 ""
  "CT" "N" "C" "O" 1 10.50 2 3.141594 ""

Now, for the CT-O2-C-O2 improper, this would map to two possible
combinations:

   [ impropers ]
   ;  atom1 atom2 atom3 atom4 phase(deg) kd(kJ/mol-1rad-2) dn
  CA    O    C OXT    180    43.932    2
  CA    OXT    C O    180    43.932    2

Are both entries required in the gromacs [ improper ] section or must I
put only one of them?


You only need one, otherwise you end up with double the intended 
strength of the improper.


-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

==

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[gmx-users] Conversion of improper angles from amber object file to gromacs

[Daniel Bauer]

Hi,

I  am trying to convert forcefield parameters of zwitterionic glycine
from an amber object file format to gromacs .rtp (to use it with
amber99sb, which lacks zwitterionic amino acids).

The amber library file I plan to use can be found here:
https://personalpages.manchester.ac.uk/staff/Richard.Bryce/amber/pro/zaa.off

This is what i have so far:

[ZG]
 [ atoms ]
 N    N3  -0.408600 1
    H1    H    0.300300 2
    H2    H    0.300300 3
    H3    H    0.300300 4
    CA    CT  -0.026400 5
   HA1    H1   0.073800 6
   HA2    H1   0.073800 7
 C    C    0.835500 8
 O    O2  -0.724500 9
   OXT    O2  -0.724500    10
 [ bonds ]
 N    H1
 N    H2
 N    H3
 N    CA
    CA   HA1
    CA   HA2
    CA C
 C O
 C    OXT

However, I am unsure about the correct conversion of impropers. In the
.off file format, those are based on the atom type, while gromacs
expects them to be based on atom names. This leaves room for some
ambiguity when the same atom type is used multiple types (i.e the COO or
NH3 group).

The improper parameter section of the .off file looks like this:

!entry.zaa_improper.parm.torsions table  str type1  str type2  str
type3  str type4  int type  dbl kp  int n  dbl p0  str desc
 "CT" "O2" "C" "O2" 1 10.50 2 3.141594 ""
 "CT" "N" "C" "O" 1 10.50 2 3.141594 ""

Now, for the CT-O2-C-O2 improper, this would map to two possible
combinations:

  [ impropers ]
  ;  atom1 atom2 atom3 atom4 phase(deg) kd(kJ/mol-1rad-2) dn
 CA    O    C OXT    180    43.932    2
 CA    OXT    C O    180    43.932    2

Are both entries required in the gromacs [ improper ] section or must I
put only one of them?


Thanks,

Daniel

-- 
Daniel Bauer, M.Sc.

TU Darmstadt
Computational Biology & Simulation
Schnittspahnstr. 2
64287 Darmstadt
ba...@cbs.tu-darmstadt.de

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[gmx-users] GROMACS has switched to use Gitlab

[Paul bauer]

Hello gmx users!

I just finished the transition of our project database to use the Gitlab 
servers.


This means that from now on issues should be reported using the issue 
tracker at https://gitlab.com/gromacs/gromacs/-/issues instead of 
redmine.gromacs.org.
The redmine and gerrit servers have been set be read only from now on, 
so that you can still access information there, but it wont be able to 
report new things there any more.


Cheers

Paul

--
Paul Bauer, PhD
GROMACS Development Manager
KTH Stockholm, SciLifeLab
0046737308594

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[gmx-users] Various questions related to Gromacs performance tuning

[Tobias Klöffel]

Dear all,
I am very new to Gromacs so maybe some of my problems are very easy to fix:)
Currently I am trying to compile and benchmark gromacs on AMD rome cpus, 
the benchmarks are taken from:

https://www.mpibpc.mpg.de/grubmueller/bench

1) OpenMP parallelization: Is it done via OpenMP tasks? If the Intel 
toolchain is detected and  -DGMX_FFT_LIBRARY=mkl is set,-mkl=serial is 
used, even though -DGMX_OPENMP=on is set.


2) I am trying to use gmx_mpi tune_pme but I never got it to run. I do 
not really understand what I have to specify for -mdrun. I tried -mdrun 
'gmx_mpi mdrun' and export MPIRUN="mpirun -use-hwthread-cpus -np $tmpi 
-map-by ppr:$tnode:node:pe=$OMP_NUM_THREADS --report-bindings" But it 
just complains that mdrun is not working.

Normal  execution via $MPIRUN gmx_mpi mdrun -s ... works


3) As far as I understood, most time of PME is spent in a 3d FFT and 
hence probably most time is spent in a mpi alltoall communication. For 
that reason I would like to place all PME tasks on a separate node via 
-ddorder pp_pme. If I do so, the calculations just hangs. Specifying 
-ddorder interleave or cartesian works without problems. Is this a known 
issue?


Kind regards,
Tobias Klöffel

--
M.Sc. Tobias Klöffel
===
HPC (High Performance Computing) group
Erlangen Regional Computing Center(RRZE)
Friedrich-Alexander-Universität Erlangen-Nürnberg
Martensstr. 1
91058 Erlangen

Room: 1.133
Phone: +49 (0) 9131 / 85 - 20101

===

E-mail: tobias.kloef...@fau.de

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[gmx-users] Lincs warning in free energy calculation

[Sadaf Rani]

Dear Gromacs users
I ran an MD simulation for 3ns and from the last coordinates started a free
energy calculation for 3ns. My system is well equilibrated but after 710725
steps I am getting Lincs warning every time as below:-

WARNING: There are no atom pairs for dispersion correction
starting mdrun 'GROtesk MACabre and Sinister in water'
150 steps,   3000.0 ps.

Step 710726, time 1421.45 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.03, max 0.23 (between atoms 5470 and 5472)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   3437   3438   43.80.1080   0.1080  0.1080

Step 710726, time 1421.45 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.03, max 0.21 (between atoms 5470 and 5472)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   3437   3438   43.10.1080   0.1080  0.1080

I have added restraints between atoms of ligand and protein and getting
Lincs warning between 1 atom included in restraints as below:-

[ bonds ]
;i j  type r0A r1A r2AfcAr0B r1B r2B
 fcB
  *3437*  790810 0.418   0.418   10.0   0.00.418   0.418   10.0
  41840.00

[ angle_restraints ]
;   aiajakal  typethA  fcAmultA  thB  fcB
 multB
  3437  7908  7906  7908   1100.29   0.01 100.29   418.40
1
  7908  3437  3439  *3437*   1146.50   0.01 146.50   418.40
  1

[ dihedral_restraints ]
;   aiajakal   typephiA dphiA  fcAphiB  dphiB
 fcB
  7906  7908  *3437*  3439 1156.16   0.00.0156.160.0
 418.40
  7907  7906  7908  *3437* 1-56.93   0.00.0-56.930.0
 418.40
  7909  *3437*  3430  3435 1131.32   0.00.0131.32 0.0
418.40

Can anyone please suggest to me how Should I fix this error? Any help will
be really appreciated.

Thanks.

Sadaf
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Re: [gmx-users] Parrinello-Rahman and Pairtype1 causing pressure instabilities

[Justin Lemkul]

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

==

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[gmx-users] Free energy change calculation

[Xiaotong Zhang]

Hi,

Sorry to bother you. Recently, I have encountered a problem when running free 
energy calculation of a dna-ligand complex system. The structure start to 
getting weird when I try to specify the two state (A,B) in the topology file, 
which is never spotted in the unconstrained MD simulations.

The version I am using is 4.6.7 and the force constant is 1000/nm/rad^2.

Could you help me with that?

Cheers

Xiaotong

Xiaotong Zhang
PGR student
x...@st-andrews.ac.uk
School of Chemistry, University of St Andrews
Purdie Building, North Haugh
St Andrews, KY16 9ST


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Re: [gmx-users] Parrinello-Rahman and Pairtype1 causing pressure instabilities

[Wesley Michaels]

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
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