[gmx-users] Gromacs Simulation in VMD
Nuno R. L. Ferreira
nunolf at ci.uc.pt
Mon Jun 6 17:34:56 CEST 2005
There's some kind of mistake here ;-)
VMD doesn't run MD simulations, it's a graphical visualizer tool, with
capacity to write your own scripts to study simulations that you fed to the
program. Yes, you can view/analyze GMX runs with VMD.
VMD has an utility called IMD that can connect to a NAMD simulation, easely
interacting/visualizing with the molecular dynamics run on the fly. NAMD
states that can use gromacs forcefields, but with some limitations.
But I still don't understand your question.
Regards
N.
----- Original Message -----
From: "Lakhani, Ahmed Ashiqali" <aalakhan at uic.edu>
To: <gmx-users at gromacs.org>
Sent: Monday, June 06, 2005 4:31 PM
Subject: [gmx-users] Gromacs Simulation in VMD
Hi Everyone,
Does anyone know, if I prepared all the file (.gro, .pdb, .top, .mdp) in
Gromacs and can I run the simulation in VMD
Ahmed Lakhani
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> Today's Topics:
>
> 1. "ideal" mdp file for NVE simulation as textbook example
> (Marc Baaden)
> 2. Re: "ideal" mdp file for NVE simulation as textbook example
> (David)
> 3. time effect of including PME calculation (Kai Zhuang)
> 4. Re: "ideal" mdp file for NVE simulation as textbook example
> (Marc Baaden)
> 5. Re: time effect of including PME calculation (David)
> 6. Re: "ideal" mdp file for NVE simulation as textbook example
> (David)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sun, 05 Jun 2005 12:00:03 +0200
> From: Marc Baaden <baaden at smplinux.de>
> Subject: [gmx-users] "ideal" mdp file for NVE simulation as textbook
> example
> To: gmx-users at gromacs.org
> Message-ID: <200506051000.j55A03D7032029 at apex.ibpc.fr>
> Content-Type: text/plain; charset="us-ascii"
>
>
> Hi,
>
> I am currently preparing/improving a tutorial on MD which is based
> on Gromacs. One of the things would be to compare a "normal" run
> to a run where all is conserved as good as possible in an NVE
> ensemble, that is the energy should be as constant as possible.
> For this I have tried the attached mdp file, with infinite cutoff,
> no constraints and no P-/T-coupling. I run it in double precision.
>
> Still the energy goes down (ca 4 kJ per 10 ps) with increasing
> noise. (See http://www.shaman.ibpc.fr/nvetest.png at the bottom)
>
> Now I wonder whether this is as good as it gets, or whether I
> overlooked some other option to avoid numerical and algorithmic
> inaccuracies ?
> (I can't run PME, I am in vacuo and charged; the system is bpti)
>
> Thanks for any suggestions,
> Marc Baaden
>
>
> -------------- next part --------------
> ;
> ; NVE test run
> ;
> title = Dynamique de BPTI
> cpp = /lib/cpp
> constraints = none
> integrator = md
> dt = 0.001 ; ps !
> nsteps = 10000 ; total 10 ps.
> nstcomm = -1
> comm-mode = ANGULAR
> nstxout = 50
> nstvout = 1000
> nstfout = 0
> nstlog = 100
> nstenergy = 100
> nstlist = 1
> ns_type = simple
> rlist = 0.0
> rcoulomb = 0.0
> rvdw = 0.0
> ; Berendsen temperature coupling is on in two groups
> Tcoupl = no
> ;Tcoupl = berendsen
> tc-grps =
> tau_t =
> ref_t =
> ; Energy monitoring
> energygrps = Protein
> ; Isotropic pressure coupling is now on
> Pcoupl = no
> ; Generate velocites is off at 300 K.
> gen_vel = no
> gen_temp = 0.0
> gen_seed = 173529
>
> pbc = no
> -------------- next part --------------
> BioMolSim meeting 2&3 Sep 2005:
> http://www.iecb.u-bordeaux.fr/satellite2005/
>
> Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris
> mailto:baaden at smplinux.de - http://www.baaden.ibpc.fr
> FAX: +33 15841 5026 - Tel: +33 15841 5176 ou +33 609 843217
>
> ------------------------------
>
> Message: 2
> Date: Sun, 05 Jun 2005 12:39:39 +0200
> From: David <spoel at xray.bmc.uu.se>
> Subject: Re: [gmx-users] "ideal" mdp file for NVE simulation as
> textbook example
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <1117967979.8480.11.camel at localhost.localdomain>
> Content-Type: text/plain
>
> On Sun, 2005-06-05 at 12:00 +0200, Marc Baaden wrote:
>> Hi,
>>
>> I am currently preparing/improving a tutorial on MD which is based
>> on Gromacs. One of the things would be to compare a "normal" run
>> to a run where all is conserved as good as possible in an NVE
>> ensemble, that is the energy should be as constant as possible.
>> For this I have tried the attached mdp file, with infinite cutoff,
>> no constraints and no P-/T-coupling. I run it in double precision.
>>
>> Still the energy goes down (ca 4 kJ per 10 ps) with increasing
>> noise. (See http://www.shaman.ibpc.fr/nvetest.png at the bottom)
>
> We have done quite a few simulations of water clusters in vacuum with
> settle that give perfect energy conservation (of course there are small
> fluctuations, but no trend like you have here). For these systems we are
> lacking all the bonded interactions of course. Maybe you want to try to
> reduce your time step to 0.2 fs (unless you have dummies). You should
> then do the same simulation length (10 ps) and compare.
>
>>
>> Now I wonder whether this is as good as it gets, or whether I
>> overlooked some other option to avoid numerical and algorithmic
>> inaccuracies ?
>> (I can't run PME, I am in vacuo and charged; the system is bpti)
>>
>> Thanks for any suggestions,
>> Marc Baaden
>>
>>
>> BioMolSim meeting 2&3 Sep 2005:
>> http://www.iecb.u-bordeaux.fr/satellite2005/
>>
>> Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris
>> mailto:baaden at smplinux.de - http://www.baaden.ibpc.fr
>> FAX: +33 15841 5026 - Tel: +33 15841 5176 ou +33 609 843217
>> _______________________________________________
>> gmx-users mailing list
>> gmx-users at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596, 75124 Uppsala, Sweden
> phone: 46 18 471 4205 fax: 46 18 511 755
> spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
>
>
> ------------------------------
>
> Message: 3
> Date: Sun, 5 Jun 2005 12:11:56 -0400
> From: Kai Zhuang <kai.zhuang at gmail.com>
> Subject: [gmx-users] time effect of including PME calculation
> To: gmx-users at gromacs.org
> Message-ID: <66c8725f05060509116f54fbed at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> hi all,
>
> I ran a system without PME and pressure coupling, 4 days or so.
> I am currently computing the exact same system with PME calculation
> and pressure coupling included, it's the 7th day now and i'm a little
> ansy as about when is it going to end and/or if i did something wrong.
>
> how much is the generaly increase of run-time due to including PME?
>
> the mdp file addition is:
>
> ;Electrostatic
> coulombtype = PME
> fourierspacing = 0.10
> pme_order = 6
> ewald_rtol = 1e-5
>
> ; Pressure coupling
> Pcoupl = berendsen
> Pcoupltype = isotropic
> tau-p = 1.0
> compressibility = 4.5e-5
> ref-p = 1.0
>
> all the rest i left the same as before.
>
> --
> Kai Zhuang
> BioMedical Engineering @ University of Toronto
> kai dot zhuang at gmail dot com
> kai.zhuang at gmail.com
> 6478314789
>
>
> ------------------------------
>
> Message: 4
> Date: Sun, 05 Jun 2005 18:24:44 +0200
> From: Marc Baaden <baaden at smplinux.de>
> Subject: Re: [gmx-users] "ideal" mdp file for NVE simulation as
> textbook example
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <200506051624.j55GOi7E031913 at apex.ibpc.fr>
> Content-Type: text/plain; charset=us-ascii
>
>
> Hi David,
>
>>>> David said:
> >> We have done quite a few simulations of water clusters in vacuum with
> >> settle that give perfect energy conservation (of course there are
> small
> >> fluctuations, but no trend like you have here). For these systems we
> are
> >> lacking all the bonded interactions of course. Maybe you want to try
> to
> >> reduce your time step to 0.2 fs (unless you have dummies). You should
> >> then do the same simulation length (10 ps) and compare.
>
> thanks for the suggestion. I tried it and indeed this seems a clear source
> of energy drift. I observe the following tendency:
>
> timestep energy drift (over 10 ps)
> -------- ------------
> 0.1 fs - 0.04 kJ/mol
> 0.2 fs - 0.15 "
> 1 fs - 4.0 "
> 2 fs - 11.7 "
>
> I'd be tempted to conclude that constant energy simulations would thus be
> rather utopic for any protein/peptide system bigger than a couple of
> residues and aiming at roughly nanosecond timescale. Or are there other
> tricks that would work (eg dummies .. but I think they'd only buy an
> order of magnitude) ?
>
> On the other hand I guess for selected system types (like the water
> cluster
> you describe) it does work.
>
> Thanks, Marc
>
> --
> BioMolSim meeting 2&3 Sep 2005:
> http://www.iecb.u-bordeaux.fr/satellite2005/
>
> Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris
> mailto:baaden at smplinux.de - http://www.baaden.ibpc.fr
> FAX: +33 15841 5026 - Tel: +33 15841 5176 ou +33 609 843217
>
>
>
>
> ------------------------------
>
> Message: 5
> Date: Sun, 05 Jun 2005 19:02:59 +0200
> From: David <spoel at xray.bmc.uu.se>
> Subject: Re: [gmx-users] time effect of including PME calculation
> To: Kai Zhuang <kai.zhuang at gmail.com>, Discussion list for GROMACS
> users <gmx-users at gromacs.org>
> Message-ID: <1117990979.4742.6.camel at localhost.localdomain>
> Content-Type: text/plain
>
> On Sun, 2005-06-05 at 12:11 -0400, Kai Zhuang wrote:
>> hi all,
>>
>> I ran a system without PME and pressure coupling, 4 days or so.
>> I am currently computing the exact same system with PME calculation
>> and pressure coupling included, it's the 7th day now and i'm a little
>> ansy as about when is it going to end and/or if i did something wrong.
>>
>> how much is the generaly increase of run-time due to including PME?
> A factor of 2-3, but here you change the pressure coupling. It is
> therefore interesting to check the density in both simulations.
>
>>
>> the mdp file addition is:
>>
>> ;Electrostatic
>> coulombtype = PME
>> fourierspacing = 0.10
>> pme_order = 6
>> ewald_rtol = 1e-5
>>
>> ; Pressure coupling
>> Pcoupl = berendsen
>> Pcoupltype = isotropic
>> tau-p = 1.0
>> compressibility = 4.5e-5
>> ref-p = 1.0
>>
>> all the rest i left the same as before.
>>
> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596, 75124 Uppsala, Sweden
> phone: 46 18 471 4205 fax: 46 18 511 755
> spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
>
>
> ------------------------------
>
> Message: 6
> Date: Sun, 05 Jun 2005 19:06:39 +0200
> From: David <spoel at xray.bmc.uu.se>
> Subject: Re: [gmx-users] "ideal" mdp file for NVE simulation as
> textbook example
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <1117991199.4742.10.camel at localhost.localdomain>
> Content-Type: text/plain
>
> On Sun, 2005-06-05 at 18:24 +0200, Marc Baaden wrote:
>> Hi David,
>>
>> >>> David said:
>> >> We have done quite a few simulations of water clusters in vacuum
>> with
>> >> settle that give perfect energy conservation (of course there are
>> small
>> >> fluctuations, but no trend like you have here). For these systems we
>> are
>> >> lacking all the bonded interactions of course. Maybe you want to try
>> to
>> >> reduce your time step to 0.2 fs (unless you have dummies). You
>> should
>> >> then do the same simulation length (10 ps) and compare.
>>
>> thanks for the suggestion. I tried it and indeed this seems a clear
>> source
>> of energy drift. I observe the following tendency:
>>
>> timestep energy drift (over 10 ps)
>> -------- ------------
>> 0.1 fs - 0.04 kJ/mol
>> 0.2 fs - 0.15 "
>> 1 fs - 4.0 "
>> 2 fs - 11.7 "
>>
>> I'd be tempted to conclude that constant energy simulations would thus
>> be
>> rather utopic for any protein/peptide system bigger than a couple of
>> residues and aiming at roughly nanosecond timescale. Or are there other
>> tricks that would work (eg dummies .. but I think they'd only buy an
>> order of magnitude) ?
> If you increase the tolerance for shake or LINCS you could also use
> constraints. The question of course is whether there is any part of the
> potential that is especially prone to energy drift.
>
>>
>> On the other hand I guess for selected system types (like the water
>> cluster
>> you describe) it does work.
> Which proves that the integration algorithm is fine, and the nonbonded
> energy functions too.
>>
>> Thanks, Marc
>>
> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596, 75124 Uppsala, Sweden
> phone: 46 18 471 4205 fax: 46 18 511 755
> spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
>
>
> ------------------------------
>
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
>
>
> End of gmx-users Digest, Vol 14, Issue 17
> *****************************************
>
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