[gmx-users] RE: Anisotropic pressure control
Matteus Lindgren
matteus.lindgren at chem.umu.se
Mon Mar 1 10:33:43 CET 2010
Thank you for the comment.
I understand your confusion. Yes, the volume of the box volume should
fluctuate with pressure control but not on the large scale that I get. The
box fluctuates and does not seem to settle on a certain volume. I have tried
with the Berendsen algorithm as well but that run crashed. When I remove the
frozen TiO2 surface the box volume does not at all fluctuate as much. It
therefore seems to be some problem with the frozen atoms and pressure
control.
Any ideas about this?
Thanks
Matteus
-----Original Message-----
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
On Behalf Of gmx-users-request at gromacs.org
Sent: den 1 mars 2010 01:18
To: gmx-users at gromacs.org
Subject: gmx-users Digest, Vol 71, Issue 1
Send gmx-users mailing list submissions to
gmx-users at gromacs.org
To subscribe or unsubscribe via the World Wide Web, visit
http://lists.gromacs.org/mailman/listinfo/gmx-users
or, via email, send a message with subject or body 'help' to
gmx-users-request at gromacs.org
You can reach the person managing the list at
gmx-users-owner at gromacs.org
When replying, please edit your Subject line so it is more specific
than "Re: Contents of gmx-users digest..."
Today's Topics:
1. simulation settings (politr at fh.huji.ac.il)
2. Re: simulation settings (Mark Abraham)
3. Question about distance restraints, energy minimization and
time averaging. (Arthur Roberts)
4. Re: Question about distance restraints, energy minimization
and time averaging. (Erik Marklund)
5. NVE of water (Andrea)
6. RE: Anisotropic pressure control (Dallas B. Warren)
----------------------------------------------------------------------
Message: 1
Date: Sun, 28 Feb 2010 15:00:11 +0200
From: politr at fh.huji.ac.il
Subject: [gmx-users] simulation settings
To: gmx-users at gromacs.org
Message-ID: <20100228150011.61721j3pdrw2efog at webmail.huji.ac.il>
Content-Type: text/plain; charset=UTF-8; DelSp="Yes";
format="flowed"
Dear Gromacs users and developers,
I want to perform simulation of peptide dissolved in water using NPT.
For constant temperature I use Berendsen temperature coupling. Do I
have to define tc-grps for 2 groups (protein and solvent) or I may use
tc-grps =System.
What is the difference? The person who introduced gromacs to me uses
tc-grps = Protein Sol_Ions
but he is not sure why it should be in this way if at all
Can you, please elucidate this issue to me.
Thank you a lot.
Regina
----------------------------------------------------------------
This message was sent using IMP, the Internet Messaging Program.
------------------------------
Message: 2
Date: Mon, 01 Mar 2010 00:50:42 +1100
From: Mark Abraham <Mark.Abraham at anu.edu.au>
Subject: Re: [gmx-users] simulation settings
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <4B8A74B2.3050206 at anu.edu.au>
Content-Type: text/plain; charset=UTF-8; format=flowed
On 1/03/2010 12:00 AM, politr at fh.huji.ac.il wrote:
> Dear Gromacs users and developers,
> I want to perform simulation of peptide dissolved in water using NPT.
> For constant temperature I use Berendsen temperature coupling. Do I have
> to define tc-grps for 2 groups (protein and solvent) or I may use
> tc-grps =System.
> What is the difference? The person who introduced gromacs to me uses
> tc-grps = Protein Sol_Ions
> but he is not sure why it should be in this way if at all
> Can you, please elucidate this issue to me.
There's some quick advice here
http://www.gromacs.org/Documentation/Terminology/Thermostats, otherwise
consult some textbook material.
Mark
------------------------------
Message: 3
Date: Sun, 28 Feb 2010 10:25:24 -0800
From: Arthur Roberts <aroberts99163 at yahoo.com>
Subject: [gmx-users] Question about distance restraints, energy
minimization and time averaging.
To: gmx users <gmx-users at gromacs.org>
Message-ID: <9ED0AA2D-C946-40BC-B85B-844962C4D2D2 at yahoo.com>
Content-Type: text/plain; charset=US-ASCII; format=flowed
Hi, all,
This is probably a very simple question. Does time averaging apply,
when distance restraints are used during energy minimization (steepest
descent or conjugate gradient)? Your input would be greatly
appreciated.
Art Roberts
Dr. Arthur Roberts, Ph.D.
University of California, San Diego
Skaggs School of Pharmacy and Pharmaceutical Sciences
9500 Gilman Drive #0703
La Jolla, CA 92093-0703
email: aroberts99163 at yahoo.com
cell: 206-850-7468
skype=aroberts92122
------------------------------
Message: 4
Date: Sun, 28 Feb 2010 20:53:38 +0100
From: Erik Marklund <erikm at xray.bmc.uu.se>
Subject: Re: [gmx-users] Question about distance restraints, energy
minimization and time averaging.
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <4B8AC9C2.3030906 at xray.bmc.uu.se>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Hi,
I'm not sure if I understand exactly what you meen, but since there's no
time propagation during energy minimization, time-averages don't make
much sense.
Erik
Arthur Roberts skrev:
> Hi, all,
>
> This is probably a very simple question. Does time averaging apply,
> when distance restraints are used during energy minimization (steepest
> descent or conjugate gradient)? Your input would be greatly
> appreciated.
>
> Art Roberts
>
> Dr. Arthur Roberts, Ph.D.
> University of California, San Diego
> Skaggs School of Pharmacy and Pharmaceutical Sciences
> 9500 Gilman Drive #0703
> La Jolla, CA 92093-0703
>
> email: aroberts99163 at yahoo.com
> cell: 206-850-7468
> skype=aroberts92122
>
>
>
--
-----------------------------------------------
Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: +46 18 471 4537 fax: +46 18 511 755
erikm at xray.bmc.uu.se http://xray.bmc.uu.se/molbiophys
------------------------------
Message: 5
Date: Sun, 28 Feb 2010 21:25:37 +0100
From: Andrea <andreamuntean at gmail.com>
Subject: [gmx-users] NVE of water
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID:
<b7d3859e1002281225k6992bb15o3ce07e370d59f7b7 at mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"
Dear users,
for test purposes in order to set up a bigger system, I try to run NVE
simulations of SPC water, but the energy increases very rapidely. My guess
is that the cutoffs I use are not good for water. I that the case ( I would
be grateful for a good reference for suitable SPC water parameters) or do I
miss something else?
My parameter file for the NVE is:
title = NVE
cpp = /lib/cpp
integrator = md
dt = 0.002 ; ps ! = 2 fs
nsteps = 50000 ; total 100 ps
nstxout = 5000
nstvout = 5000
nstxtcout = 0
nstlog = 5000
nstenergy = 5000
nstlist = 10
ns_type = grid
rlist = 1.1
unconstrained-start = yes
constraints = all-bonds
constraint_algorithm = shake
shake_tol = 0.0001
;VdW
vdwtype = Switch
rvdw = 1.0 ; rvdw+ (0.1:0.3)= rlist
rvdw_switch = 0.9
gen_vel = no ; yes
gen_temp = 300
gen_seed = -1
;Temperature coupling
tc_grps = system
tcoupl = no ;nose-hoover
tau_t = 0.1
ref_t = 300
;Pressure coupling
pcoupl = no
optimize_fft = yes
Any suggesions are really welcome.
Thank you.
Regards,
Andrea Muntean
-------------- next part --------------
An HTML attachment was scrubbed...
URL:
http://lists.gromacs.org/pipermail/gmx-users/attachments/20100228/d6163c93/a
ttachment-0001.html
------------------------------
Message: 6
Date: Mon, 01 Mar 2010 11:11:06 +1100
From: "Dallas B. Warren" <Dallas.Warren at pharm.monash.edu.au>
Subject: RE: [gmx-users] Anisotropic pressure control
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID:
<89907EA1DCFB7548A431C13A270F9DD509398282 at prk-exch-01.vcp.local>
Content-Type: text/plain; charset="iso-8859-1"
Why is it that what you have run with xy rigid and z couple not correct?
Fluctuating box volume is exactly what you would expect to get, and do get,
with pressure coupling.
Catch ya,
Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at pharm.monash.edu.au
+61 3 9903 9167
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a
nail.
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
On Behalf Of Matteus Lindgren
Sent: Friday, 26 February 2010 8:24 PM
To: gmx-users at gromacs.org
Subject: [gmx-users] Anisotropic pressure control
Dear experts,
I am trying to run MD on a protein in water above a flat surface of TiO2 in
a cubic box with pressure control. All the atoms of TiO2 are frozen and I
therefore think that anisotropic pressure control must be used. I tried
allowing box fluctuations in the direction of the normal vector (the z-axis)
of the TiO2 surface but the box volume then oscillates during the whole
simulation. The same parameters worked for a simulation of protein+water
without the frozen TiO2 surface.
How can I use pressure control for a system with a frozen surface that
extends through the whole box? Ive read the posts about membrane simulations
but membranes are flexible so I think those suggestions might not apply.
The important part of the input file was as follows:
nstlist = 10
ns_type = grid
pbc = xyz
periodic_molecules = no
rlist = 1.2
coulombtype = PME
rcoulomb-switch = 0
rcoulomb = 1.2
epsilon-r = 1
epsilon_rf = 1
vdw-type = Cut-off
rvdw-switch = 0
rvdw = 1.4
DispCorr = EnerPres
table-extension = 1.5
energygrp_table =
fourierspacing = 0.12
pme_order = 4
ewald_rtol = 1e-05
ewald_geometry = 3d
optimize_fft = yes
Tcoupl = Nose-hoover
tc-grps = protres RUT solcl
tau_t = 0.1 0.1 0.1
ref_t = 310 310 310
Pcoupl = Parrinello-Rahman
Pcoupltype = anisotropic
tau_p = 2.0 2.0 2.0 2.0 2.0 2.0
compressibility = 0.0 0.0 5e-5 0.0 0.0 0.0
ref_p = 0 0 1.01325 0 0 0
gen_vel = yes
gen_temp = 310
gen_seed = 1993
constraints = hbonds
constraint-algorithm = lincs
continuation = yes
lincs-order = 4
lincs-iter = 4
freezegrps = frozen
freezedim = Y Y Y
Thanks
Matteus
---------------------------------------------------------
Matteus Lindgren, graduate student
Department of Chemistry, Umee University
SE-901 87 Umee, Sweden
Phone: +46 (0)90-7865368
-------------- next part --------------
An HTML attachment was scrubbed...
URL:
http://lists.gromacs.org/pipermail/gmx-users/attachments/20100301/7e534794/a
ttachment.html
------------------------------
--
gmx-users mailing list
gmx-users at gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
End of gmx-users Digest, Vol 71, Issue 1
****************************************
More information about the gromacs.org_gmx-users
mailing list