[gmx-users] perl scripts to convert CHARMM ff in GROMACS: [solved]
ABEL Stephane 175950
Stephane.ABEL at cea.fr
Tue Feb 2 09:35:01 CET 2010
Hi,
With the Mark Abraham's scripts and advices, I have finally resolved my problems.
Thank you and see ya on the list
Stéphane
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Objet : gmx-users Digest, Vol 70, Issue 7
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Today's Topics:
1. Fwd: Help for REMD (Mark Abraham)
2. Re: perl scripts to convert CHARMM ff in GROMACS (Mark Abraham)
3. Re: density problems when switching from md to sd integrator
(Aymeric Na?m?)
4. RE: Re: density problems when switching from md to sd
integrator (Berk Hess)
5. [OT] Software package for discontinuous molecular dynamics?
(DMD) (ms)
----------------------------------------------------------------------
Message: 1
Date: Tue, 02 Feb 2010 01:45:01 +1100
From: Mark Abraham <Mark.Abraham at anu.edu.au>
Subject: [gmx-users] Fwd: Help for REMD
To: Gromacs Users <gmx-users at gromacs.org>
Message-ID: <4B66E8ED.8030403 at anu.edu.au>
Content-Type: text/plain; charset=iso-8859-9; format=flowed
Please keep GROMACS correspondence on the mailing list. Nobody here is a
private tutor unless you're paying them.
-------- Original Message --------
Subject: Help for REMD
Date: Mon, 01 Feb 2010 14:58:08 +0200 (EET)
From: Murat Erman OGUZ <erman at hacettepe.edu.tr>
To: mark.abraham at anu.edu.au
Dear Mr.Mark Abraham
I am Erman Oguz from Turkey Hacettepe University.
I have a problem about Replica Excahange Method on Gromacs.
ý hope you can help me.
I am trying to perform replica exchange MD on a 'protein in
water' system. I have to perform the REMD simulation with 64 different
temperatures.As per advise on wiki,I equilibrated the system at
respective temperatures (total of 64 equilibration simulations in 200 ps).
After this I generated "tpr files" from the equilibrated structure.
when I submit final job for REMD with following command-line
command line: mpirun -np 64 mdrun -multi 64 -replex 1000 -s *_.tpr .....
it gives error that :
t=29.802 ps Water molecule starting at atom 5902 can not be settled.
check for bad contacs and/or reduce time step.
what can I do and how can I do... please help me...
You should start by searching on the GROMACS webpage errors page. The
reasons for this kind of error are clearly described there, and are
likely to have nothing to with REMD as such. If they were, you'll have
to provide much more data for anyone to help.
You should try your .tpr files in a non-replica simulation and see which
are broken and thus what to do about it. Probably you've not
equilibrated well enough, or have a broken system, or have a temperature
range that is too great for your integration to be stable at high T.
Mark
------------------------------
Message: 2
Date: Tue, 02 Feb 2010 01:54:13 +1100
From: Mark Abraham <Mark.Abraham at anu.edu.au>
Subject: Re: [gmx-users] perl scripts to convert CHARMM ff in GROMACS
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <4B66EB15.5090706 at anu.edu.au>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 02/02/10 01:29, ABEL Stephane 175950 wrote:
> Hi GMXusers
>
> I am testing the parameters of CHARMM, it works fine for lipids and protein. This is a great job, thanks to the devellopers But i would like to add some new molecule for solvent (e.g. for TFE) The atom types of TFE are present in the ffcharmm27bon.itp available in latest port (c32b1_release_1.1.zip, dowloaded http://www.dbb.su.se/User:Bjelkmar/Ffcharmm), unfortunately several bonded parameters (for example F3-CF3, CF3-CT2x, etc..) are missing in ffcharmm27bon.itp file. So I need to convert the missing parameters into gromacs format. In website (URL:http://www.gromacs.org/@api/deki/files/76/=charmm_to_gromacs.tgz), I have found that several perl scripts exist for the conversion charmm--> gromacs. The archive is corrupted so, I cannot unpacked the directory to obtain the files.
>
> Where I can find these scripts
Emailed off-list. This package is now deprecated.
Mark
------------------------------
Message: 3
Date: Mon, 01 Feb 2010 16:58:44 +0100
From: Aymeric Na?m? <anaome at fundp.ac.be>
Subject: [gmx-users] Re: density problems when switching from md to sd
integrator
To: gmx-users at gromacs.org
Message-ID: <4B66FA34.40808 at fundp.ac.be>
Content-Type: text/plain; charset="iso-8859-1"
I have changed tau_t=0.2 for 1.0 but the density is not restored. I have tried with the parameters from Villa and Mark (J Comput Chem, 2002, 23, 548)
, tau_t=0.2 and tau_p=2.0 and still get the same density. The self-diffusion coefficient is indeed half of that with md with sd and tau_t=0.2 (0.71 vs. 1.48 10-5 cm2/s)
and about the same with tau_t=1.0 (1.57 10-5 cm2/s). Water is less affected (1009 g/L with md and 1007 g/L with sd and tau_t=0.2). What is the reason why the density is lowered?
Here is the .mdp file (for the simulation with md, tau_t=0.1):
title = cyclohexane
cpp = /lib/cpp -traditional
define = -DFLEXIBLE
constraints = none
integrator = sd
dt = 0.001 ; fs !
nsteps = 2000000 ; total 2000 ps.
nstcomm = 1
nstxout = 1000
nstvout = 1000
nstfout = 0
nstlog = 500
nstenergy = 500
nstlist = 10
ns_type = grid
rlist = 1.0
coulombtype = PME
rcoulomb = 1.0
rvdw = 1.4
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 6
ewald_rtol = 1e-5
optimize_fft = yes
energygrps = system
; Berendsen temperature coupling is on in three groups
Tcoupl = berendsen
tau_t = 0.2
tc_grps = System
ref_t = 298
; Pressure coupling is on
Pcoupl = berendsen
pcoupltype = isotropic
tau_p = 0.5
compressibility = 11.2e-5
ref_p = 1.0
; Generate velocites is on at 300 K.
gen_vel = no
gen_temp = 298.0
gen_seed = 173529
; Energy group exclusion
energygrp_excl =
freezegrps =
freezedim =
; Non-equilibrium Thermodynamics
acc_grps =
accelarate =
; center of mass
comm_mode =
comm_grps =
> Dear Aymeric:
>
> 1. Can we please see the entire .mdp files for both simulations? I
> suggest that you use a tau_t=1.0 (0.2 is probably over-damped).
>
> 2. Although any value of tau_t should still produce the correct
> equilibria, your diffusion rates and your overall sampling may be
> slower with sd tau_t=0.2 than they are with md.
>
> 3. Can you reproduce this effect with a box of water?
>
>> -- original message --
>>
>> I'm simulating a box of cyclohexane (GROMOS 53a6, 512 molecules, 298K,
>> compressibility=11.2 10-5 bar-,1 tau_p=0.5 ps, no constraints on bonds).
>> After equilibration and NPT simulation, the system reaches the proper
>> density reported for the model (791g/L). When I switch to a stochastic
>> integrator (with inverse friction coeff. tau_t=0.2 ps) the density
>> rapidly falls to about 765g/L, the potential energy increases, while
>> temperature and pressure fluctuate much more around their specified
>> values. I intend to use this box of cyclohexane for solvation free
>> energy calculations. Can anyone explain what is going on?
>> Thanks in advance
>>
>> Aymeric
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Message: 4
Date: Mon, 1 Feb 2010 17:21:05 +0100
From: Berk Hess <gmx3 at hotmail.com>
Subject: RE: [gmx-users] Re: density problems when switching from md
to sd integrator
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <COL113-W5083351CC512A074C196978E580 at phx.gbl>
Content-Type: text/plain; charset="iso-8859-1"
Hi,
This force field was designed to be used with constraints.
First try running with constraints set to all-bonds and without -DFLEXIBLE and check
the densities again.
Berk
> Date: Mon, 1 Feb 2010 16:58:44 +0100
> From: anaome at fundp.ac.be
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Re: density problems when switching from md to sd integrator
>
> I have changed tau_t=0.2 for 1.0 but the density is not restored. I have tried with the parameters from Villa and Mark (J Comput Chem, 2002, 23, 548)
> , tau_t=0.2 and tau_p=2.0 and still get the same density. The self-diffusion coefficient is indeed half of that with md with sd and tau_t=0.2 (0.71 vs. 1.48 10-5 cm2/s)
> and about the same with tau_t=1.0 (1.57 10-5 cm2/s). Water is less affected (1009 g/L with md and 1007 g/L with sd and tau_t=0.2). What is the reason why the density is lowered?
>
> Here is the .mdp file (for the simulation with md, tau_t=0.1):
>
> title = cyclohexane
> cpp = /lib/cpp -traditional
> define = -DFLEXIBLE
> constraints = none
> integrator = sd
> dt = 0.001 ; fs !
> nsteps = 2000000 ; total 2000 ps.
> nstcomm = 1
> nstxout = 1000
> nstvout = 1000
> nstfout = 0
> nstlog = 500
> nstenergy = 500
> nstlist = 10
> ns_type = grid
> rlist = 1.0
> coulombtype = PME
> rcoulomb = 1.0
> rvdw = 1.4
> fourierspacing = 0.12
> fourier_nx = 0
> fourier_ny = 0
> fourier_nz = 0
> pme_order = 6
> ewald_rtol = 1e-5
> optimize_fft = yes
> energygrps = system
> ; Berendsen temperature coupling is on in three groups
> Tcoupl = berendsen
> tau_t = 0.2
> tc_grps = System
> ref_t = 298
> ; Pressure coupling is on
> Pcoupl = berendsen
> pcoupltype = isotropic
> tau_p = 0.5
> compressibility = 11.2e-5
> ref_p = 1.0
> ; Generate velocites is on at 300 K.
> gen_vel = no
> gen_temp = 298.0
> gen_seed = 173529
> ; Energy group exclusion
> energygrp_excl =
> freezegrps =
> freezedim =
> ; Non-equilibrium Thermodynamics
> acc_grps =
> accelarate =
> ; center of mass
> comm_mode =
> comm_grps =
>
> > Dear Aymeric:
> >
> > 1. Can we please see the entire .mdp files for both simulations? I
> > suggest that you use a tau_t=1.0 (0.2 is probably over-damped).
> >
> > 2. Although any value of tau_t should still produce the correct
> > equilibria, your diffusion rates and your overall sampling may be
> > slower with sd tau_t=0.2 than they are with md.
> >
> > 3. Can you reproduce this effect with a box of water?
> >
> >> -- original message --
> >>
> >> I'm simulating a box of cyclohexane (GROMOS 53a6, 512 molecules, 298K,
> >> compressibility=11.2 10-5 bar-,1 tau_p=0.5 ps, no constraints on bonds).
> >> After equilibration and NPT simulation, the system reaches the proper
> >> density reported for the model (791g/L). When I switch to a stochastic
> >> integrator (with inverse friction coeff. tau_t=0.2 ps) the density
> >> rapidly falls to about 765g/L, the potential energy increases, while
> >> temperature and pressure fluctuate much more around their specified
> >> values. I intend to use this box of cyclohexane for solvation free
> >> energy calculations. Can anyone explain what is going on?
> >> Thanks in advance
> >>
> >> Aymeric
>
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Message: 5
Date: Mon, 01 Feb 2010 16:32:39 +0100
From: ms <devicerandom at gmail.com>
Subject: [gmx-users] [OT] Software package for discontinuous molecular
dynamics? (DMD)
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <4B66F417.5090306 at gmail.com>
Content-Type: text/plain; charset=UTF-8
Hi,
Sorry for the offtopic but Google/literature quick search is not helping
and I'd like to have some more informed opinion.
To my understanding, GROMACS isn't capable of discontinuous molecular
dynamics. Is there any more-or-less standard software package for that?
thank you!
m.
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