[gmx-users] Re: gmx-users Digest, Vol 28, Issue 28
anwar at cdfd.org.in
anwar at cdfd.org.in
Thu Aug 10 12:58:47 CEST 2006
---------REPLY TO-------------
Date:Wed Aug 09 18:00:10 GMT+08:00 2006
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Subject: gmx-users Digest, Vol 28, Issue 28
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Today's Topics:
1. Re: vacuum simulation problem (Gerrit Groenhof (RUG))
2. Re: vacuum simulation problem (David van der Spoel)
3. Re: simulation at particular pH (Vojt?ch Spiwok)
4. Re: simulation at particular pH (Marc Baaden)
----------------------------------------------------------------------
Message: 1
Date: Wed, 09 Aug 2006 10:44:40 +0200
From: "Gerrit Groenhof (RUG)" <g.groenhof at rug.nl>
Subject: Re: [gmx-users] vacuum simulation problem
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <44D9A078.6020406 at rug.nl>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Hi again,
Yes, I have calculated the rmsd for individual domains and on of the individual
domains not intact. So, it is clear that the rmsd is not due to the domain
motion, but due to the structural changes with in the domain.
This dynamics was run without any periodic boundaries. Later I have submitted
another dynamics having defined a box (dictance 0.7 A) and comm_mode =
Angular. 8ns of dynamics has been done and on analysis in vmd the structure
is not rotating and the rmsd is alsostablizing after 1ns at around 5 A.
There are no drasrtic structural changes seen.
However, I think it is better if I run the dynamics without pressure coupling
as you have suggested.
Give me suggestions.
regards
Anwar
In addition to Erik and my suggestions, you should also remove the
overall rotation: comm_mode=linear.
anwar at cdfd.org.in wrote:
>Dear all,
>I am simulating a protein containing 2 domains which are linked together
>by a loop of around 10 residues. When I am simulating the same in vacuum,
>after approx 1ns, the rmsd has increased from 5 angstroms to 25 angstroms
>with in 10 time steps. You can surely imagine how drastic the structural
>changes are happening. And also during the simulation after 500ps the
protein
>started to rotate and later at approx 2ns the protein stopped rotation.
>What exactly might be happening there, why the protein is behaving like
>that. I am pasting the mdp file below.
>; User spoel (236)
>; Wed Nov 3 17:12:44 1993
>; Input file
>;
>title = Yo
>cpp = /lib/cpp
>constraints = all-bonds
>;define = -DPOSRES
>integrator = md
>dt = 0.002 ; ps !
>nsteps = 10000000 ; total 10000 ps.
>nstcomm = 1
>nstxout = 500
>nstvout = 500
>nstfout = 500
>nstlog = 500
>nstenergy = 500
>nstlist = 10
>ns_type = grid
>rlist = 0.9
>rcoulomb = 0.9
>rvdw = 0.9
>; Berendsen temperature coupling is on in two groups
>Tcoupl = berendsen
>tc-grps = Protein
>tau_t = 0.1
>ref_t = 300
>; Energy monitoring
>energygrps = Protein
>; Isotropic pressure coupling is now on
>Pcoupl = berendsen
>Pcoupltype = isotropic
>tau_p = 0.5
>compressibility = 4.5e-5
>ref_p = 1.0
>; Generate velocites is off at 300 K.
>gen_vel = no
>gen_temp = 300.0
>gen_seed = 173529
>
>
>kindly guide me in this issue.
>regards
>Anwar
>
>----------------------
>Mohd Anwaruddin
>Project Assistant
>C/o DR.H.A.Nagarajaram
>Lab of Computational Biology and Bioinformatics
>Center for DNA Fingerprinting and Diagnostics(CDFD)
>Nacharam
>Hyderabad-500 076
>INDIA.
>Tel: +91-8413-235467,68,69,70 ext 2019
>anwar.m1 at gmail.com
>-----------------------
>
>
>
>-
>
>_______________________________________________
>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
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>
>
------------------------------
Message: 2
Date: Wed, 09 Aug 2006 10:44:32 +0200
From: David van der Spoel <spoel at xray.bmc.uu.se>
Subject: Re: [gmx-users] vacuum simulation problem
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <44D9A070.4090402 at xray.bmc.uu.se>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
anwar at cdfd.org.in wrote:
> Dear all,
> I am simulating a protein containing 2 domains which are linked together
> by a loop of around 10 residues. When I am simulating the same in vacuum,
> after approx 1ns, the rmsd has increased from 5 angstroms to 25 angstroms
> with in 10 time steps. You can surely imagine how drastic the structural
> changes are happening. And also during the simulation after 500ps the
protein
> started to rotate and later at approx 2ns the protein stopped rotation.
> What exactly might be happening there, why the protein is behaving like
> that. I am pasting the mdp file below.
As Gerrit said, remove pressure coupling in vacuo and remove angular
center of mass motion.
> ; User spoel (236)
> ; Wed Nov 3 17:12:44 1993
> ; Input file
> ;
> title = Yo
> cpp = /lib/cpp
> constraints = all-bonds
> ;define = -DPOSRES
> integrator = md
> dt = 0.002 ; ps !
> nsteps = 10000000 ; total 10000 ps.
> nstcomm = 1
> nstxout = 500
> nstvout = 500
> nstfout = 500
> nstlog = 500
> nstenergy = 500
> nstlist = 10
> ns_type = grid
> rlist = 0.9
> rcoulomb = 0.9
> rvdw = 0.9
> ; Berendsen temperature coupling is on in two groups
> Tcoupl = berendsen
> tc-grps = Protein
> tau_t = 0.1
> ref_t = 300
> ; Energy monitoring
> energygrps = Protein
> ; Isotropic pressure coupling is now on
> Pcoupl = berendsen
> Pcoupltype = isotropic
> tau_p = 0.5
> compressibility = 4.5e-5
> ref_p = 1.0
> ; Generate velocites is off at 300 K.
> gen_vel = no
> gen_temp = 300.0
> gen_seed = 173529
>
>
> kindly guide me in this issue.
> regards
> Anwar
>
> ----------------------
> Mohd Anwaruddin
> Project Assistant
> C/o DR.H.A.Nagarajaram
> Lab of Computational Biology and Bioinformatics
> Center for DNA Fingerprinting and Diagnostics(CDFD)
> Nacharam
> Hyderabad-500 076
> INDIA.
> Tel: +91-8413-235467,68,69,70 ext 2019
> anwar.m1 at gmail.com
> -----------------------
>
>
>
> -
>
> _______________________________________________
> 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.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
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://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
------------------------------
Message: 3
Date: Wed, 09 Aug 2006 10:49:30 +0200
From: Vojt?ch Spiwok <Vojtech.Spiwok at vscht.cz>
Subject: [gmx-users] Re: simulation at particular pH
To: gmx-users at gromacs.org
Message-ID: <44D9A19A.5030700 at vscht.cz>
Content-Type: text/plain; charset=UTF-8; format=flowed
Dear Luisa
The web tool propKa http://propka.chem.uiowa.edu/
might be useful in prediction of protonation states
of your protein at givven pH. Simulation with a
constant pH (with dynamic protonation state
assignment) was reported and might be an idea
for further gromacs development.
Vojtech
>
> Hello to everybody,
> I am new to this mailing list and I am writing because I wonder if anybody
knows how can I set up the pH of the system in gramacs.
> Thank you to everybody
> Luisa
------------------------------
Message: 4
Date: Wed, 09 Aug 2006 10:33:51 +0200
From: Marc Baaden <baaden at smplinux.de>
Subject: Re: [gmx-users] simulation at particular pH
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <200608090833.k798Xp0e003601 at apex.ibpc.fr>
Content-Type: text/plain; charset=us-ascii
Hi,
I would like to add a little nuance to Gerrit's answer. Although he is
right
that there is currently no way of accurately and generally modeling acidity
by introducing explicit H3O+/OH-, one can still use that approach to check
the groce effect in benign cases, like eg if you were to investigate an
industrial process at 1 M acid. At least we tried so in the past [1] and
got
some interesting results.
Marc
[1] TBP at the water - oil interface: the effect of TBP concentration and
water acidity investigated by molecular dynamics simulations
J. Phys. Chem. B, 105, 2001, 11131-11141
>>> Gerrit Groenhof said:
>> Bad idea. Adding just one proton (1/Navogadro moles ~ 1.6 * 10^-24)to
a
>> box of say 500 nm^3 (5 10^-22 liter), continaining roughly 10000 waters
>> would give a pH of 2.5 (-log[1.6/5*10^-2), which is the maximum pH you
>> can reach for such standard box. If you want to go higher, say to pH=7,
>> your box needs to be at least 1.6 * 10^-17 liter, or 1.6 * 10^7 nm^3.
>> THis is too big for simulation.
>>
>> Therefore adding H+ or H3O+ is not really an option. Instead you should
>> choose the protonation states of the titrating sites in the system such
>> that they correspond to the pH your are interested in. Equilibrium
>> exchange of protons between aminoacid sidechains is probably happening
>> on a timescale much longer than a typical simulation length.
>>
>> Gerrit
--
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
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