RE: [gmx-users] Viscosity in PE
Thanx!
Alessandro Mattozzi
M.Phil., Ph.D. student
Dept. of Fibre and Polymer Technology
Royal Institute of Technology
Stockholm, Sweden
-Original Message-
From: [EMAIL PROTECTED] on behalf of Berk Hess
Sent: Fri 9/8/2006 8:34 AM
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] Viscosity in PE
From: David van der Spoel [EMAIL PROTECTED]
Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org
To: Discussion list for GROMACS users gmx-users@gromacs.org
Subject: Re: [gmx-users] Viscosity in PE
Date: Thu, 07 Sep 2006 19:36:34 +0200
Esther Caballero-Manrique wrote:
You can calculate it from the velocity autocorrelation function, which can
be calculated using the g_velacc. The friction can be calculated from the
integral of the velocity autocorrelation function (friction=3KbT/(integral
of vacf)) and then the viscosity can be calculated using Stoke's equation
(friction=6 x PI x visc x radius). But you need to have saved the
velocities fairly often (say every 5 fs?). This came up recently in the
mailing lists, you can search the velocity autocorrelation function. This
method integrates the integral at time infinite (ie, see Morriss and
Evan's book /Statistical Mechanics of Nonequilibrium Liquids, /now on the
web @ http://rsc.anu.edu.au/~evans/evansmorrissbook.htm) which might or
might not be a good approximation for your system. Otherwise you can do
more sophisticated methods such as those outlined in chapter 6 of the
manual.
Hope it helps,
Esther
An alternative method that is implemented requires non-equibrium
simulations. Check out
@Article{Hess2002b,
author = {B. Hess},
title = {Determining the shear viscosity of model liquids from
molecular simulation},
journal ={J. Chem. Phys.},
year = 2002,
volume = 116,
pages = {209-217}
}
you have to set cos_acceleration in the mdp to e.g. 0.1 nm/ps^2
In Gromacs viscosity calculations can be done with several methods,
all of which are described in the paper mentioned above.
But for PE-1000 it is not that straightforward as for a simple liquid.
The system has very long relaxation times and the viscosity will be
very non-linear in the shear rate.
You should read some literature on viscosity calculations in polymer melts.
Berk.
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Re: [gmx-users] Measuring Atom Distances
Title: Re: [gmx-users] Measuring Atom Distances Hi all let's say that I have two subset of atoms, let's call them i, j, k (first group A) and l, m, n (second group B). Is there any elegant way (rather than iterating g_dist) of having the average over the trajectory and over ALL the possible permutation over the two subset A and B. Thanx Regards Alessandro Mattozzi M.Phil., Ph.D. student Dept. of Fibre and Polymer Technology Royal Institute of Technology Stockholm, Sweden -Original Message- From: [EMAIL PROTECTED] on behalf of Tsjerk Wassenaar Sent: Tue 7/4/2006 9:40 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Measuring Atom Distances Hi Javad, You don't need to bother using make_ndx, just create a file atoms.ndx which reads like this: [ atom1 ] number_of _first_atom [ atom2 ] number_of_second_atom Cheers, Tsjerk On 7/4/06, Javad Azadi [EMAIL PROTECTED] wrote: Is it just a matter of using make_ndx -f traj.gro a (atom1 number from .gro) (atom2 number from .gro) then selecting keep # where # is the index just created? Javad Dallas B. Warren [EMAIL PROTECTED] said: I tried g_dist, and the out put is nothing but zeros. I only have the two unconnected atoms indexed that I want to measure, could that be the problem? I would check what you are doing. It shouldn't matter whether the atoms are connected or not, g_dist will measure the distance between them. Are you sure you have set up the index groups correctly? Catch ya, Dr. Dallas Warren Lecturer Department of Pharmaceutical Biology and Pharmacology Victorian College of Pharmacy, Monash University 381 Royal Parade, Parkville VIC 3010 [EMAIL PROTECTED] +61 3 9903 9524 - When the only tool you own is a hammer, every problem begins to resemble a nail. ___ gmx-users mailing list gmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- ___ gmx-users mailing list gmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, M.Sc. Groningen Biomolecular Sciences and Biotechnology Institute (GBB) Dept. of Biophysical Chemistry University of Groningen Nijenborgh 4 9747AG Groningen, The Netherlands +31 50 363 4336 ___ gmx-users mailing list gmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Van der Waals: switch attractive term off
I apologise if my lack of clarity caused the birth of an hermeneutic thread. I 'll try my best next time :-) Regards Alessandro Mattozzi M.Phil., Ph.D. student Dept. of Fibre and Polymer Technology Royal Institute of Technology Stockholm, Sweden winmail.dat___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Measuring Atom Distances
Hi all let's say that I have two subset of atoms, let's call them i, j, k (first group A) and l, m, n (second group B). Is there any elegant way (rather than iterating g_dist) of having the average over the trajectory and over ALL the possible permutation over the two subset A and B. Regards Alessandro Mattozzi M.Phil., Ph.D. student Dept. of Fibre and Polymer Technology Royal Institute of Technology Stockholm, Sweden -Original Message- From: [EMAIL PROTECTED] on behalf of Tsjerk Wassenaar Sent: Tue 7/4/2006 9:40 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Measuring Atom Distances Hi Javad, You don't need to bother using make_ndx, just create a file atoms.ndx which reads like this: [ atom1 ] number_of _first_atom [ atom2 ] number_of_second_atom Cheers, Tsjerk On 7/4/06, Javad Azadi [EMAIL PROTECTED] wrote: Is it just a matter of using make_ndx -f traj.gro a (atom1 number from .gro) (atom2 number from .gro) then selecting keep # where # is the index just created? Javad Dallas B. Warren [EMAIL PROTECTED] said: I tried g_dist, and the out put is nothing but zeros. I only have the two unconnected atoms indexed that I want to measure, could that be the problem? I would check what you are doing. It shouldn't matter whether the atoms are connected or not, g_dist will measure the distance between them. Are you sure you have set up the index groups correctly? Catch ya, Dr. Dallas Warren Lecturer Department of Pharmaceutical Biology and Pharmacology Victorian College of Pharmacy, Monash University 381 Royal Parade, Parkville VIC 3010 [EMAIL PROTECTED] +61 3 9903 9524 - When the only tool you own is a hammer, every problem begins to resemble a nail. ___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- ___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, M.Sc. Groningen Biomolecular Sciences and Biotechnology Institute (GBB) Dept. of Biophysical Chemistry University of Groningen Nijenborgh 4 9747AG Groningen, The Netherlands +31 50 363 4336 ___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php winmail.dat___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Compiling;Van der Waals: switch attractive term off
Thanks! How should I do it? Is force.c used by grompp or mdrun? I want to know if I can run on shared resources (by just preprocessing with the edited version) or I do have to run it locally. Regards A newbie Alessandro Mattozzi M.Phil., Ph.D. student Dept. of Fibre and Polymer Technology Royal Institute of Technology Stockholm, Sweden -Original Message- From: [EMAIL PROTECTED] on behalf of Pradip Kumar Biswas Sent: Fri 6/30/2006 8:27 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Van der Waals: switch attractive term off It seems that you can modify the following line in the function *mk_nbfp() in force.c and achieve what you want. C6(nbfp,atnr,i,j) = idef-iparams[k].lj.c6; (it is in line 117 of force.c in version 3.3) and change it to C6(nbfp,atnr,i,j) = 0; This will set the attractive interaction between atom i j to 0. pb. On Jun 30, 2006, at 4:14 AM, Alessandro Mattozzi wrote: Hi All I simulate PE using AUA. I would like to switch the attractive term of the vdW force. How can I do it? Regards Alessandro Mattozzi M.Phil., Ph.D. student Dept. of Fibre and Polymer Technology Royal Institute of Technology Stockholm, Sweden ___ gmx-users mailing list gmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Pradip K. Biswas, PhD. Research Associate, Department of Chemistry; Cleveland State University, Ohio-44115 Phone: 1-216-875-9723 http://comppsi.csuohio.edu/groups/people/biswas.html winmail.dat___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Compiling;Van der Waals: switch attractive term off
My idea is to do as suggested by van der Vegt in 1996JChPh.105.8849V. The attractive part of the LJ is turn off to avoid monomers from sticking together. Regards Alessandro Mattozzi M.Phil., Ph.D. student Dept. of Fibre and Polymer Technology Royal Institute of Technology Stockholm, Sweden -Original Message- From: [EMAIL PROTECTED] on behalf of Berk Hess Sent: Mon 7/3/2006 10:55 AM To: gmx-users@gromacs.org Subject: RE: [gmx-users] Compiling;Van der Waals: switch attractive term off From: Alessandro Mattozzi [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: Discussion list for GROMACS users gmx-users@gromacs.org Subject: RE: [gmx-users] Compiling;Van der Waals: switch attractive term off Date: Mon, 3 Jul 2006 10:40:18 +0200 Thanks! How should I do it? Is force.c used by grompp or mdrun? I want to know if I can run on shared resources (by just preprocessing with the edited version) or I do have to run it locally. I think you did not answer to my question yet. For coarse-grained polymer models one usually sets the LJ force to zero after the minimum. But I don't know what you want to do exactly, so maybe you really want to turn of the 1/r^6 term. I that case it seems a bit complicated to me to edit Gromacs source code. For a simple polymer you just have a few LJ parameters, so I guess it is easier to just set all C6 parameters to zero in the force field file. If you use sigma and epsilon entries, it is little work to change these to C6/C12 values. The manual describes how to do this. Berk. ___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php winmail.dat___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Compiling;Van der Waals: switch attractive term off
thanks! Alessandro Mattozzi M.Phil., Ph.D. student Dept. of Fibre and Polymer Technology Royal Institute of Technology Stockholm, Sweden -Original Message- From: [EMAIL PROTECTED] on behalf of Berk Hess Sent: Mon 7/3/2006 11:36 AM To: gmx-users@gromacs.org Subject: RE: [gmx-users] Compiling;Van der Waals: switch attractive term off From: Alessandro Mattozzi [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: Discussion list for GROMACS users gmx-users@gromacs.org Subject: RE: [gmx-users] Compiling;Van der Waals: switch attractive term off Date: Mon, 3 Jul 2006 11:15:48 +0200 My idea is to do as suggested by van der Vegt in 1996JChPh.105.8849V. The attractive part of the LJ is turn off to avoid monomers from sticking together. Van der Vegt is my supervisor. I just called him to ask what he did. Setting all C6 parameters to zero would accomplish what you want. So you can set them to zero in the force field/topology file or edit the code. As I said, I guess the first thing would be easier. Berk. ___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php winmail.dat___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_dist
Title: g_dist Hi all how reacts g_dist if one group contents 3 segments of three identical molecules. Are the distances calculated referring to the centers of mass of the single molecules segments and then averaged or referring to the center of mass of the set of the three segments? Regards Alessandro Mattozzi M.Phil., Ph.D. student Dept. of Fibre and Polymer Technology Royal Institute of Technology Stockholm, Sweden ___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Van der Waals: switch attractive term off
Title: Van der Waals: switch attractive term off Hi All I simulate PE using AUA. I would like to switch the attractive term of the vdW force. How can I do it? Regards Alessandro Mattozzi M.Phil., Ph.D. student Dept. of Fibre and Polymer Technology Royal Institute of Technology Stockholm, Sweden ___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_com
Title: g_com Hi Is there any way for calculating the trajectory of the center of mass ? Alessandro Mattozzi M.Phil., Ph.D. student Dept. of Fibre and Polymer Technology Royal Institute of Technology Stockholm, Sweden ___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Trajectory sampling- NPT or NVT?
Title: Trajectory sampling- NPT or NVT? Hi all I am running diffusion simulation. When collecting my penetrant trajectories, shall I use NPT or NVT dynamics? It looks like references are divided about that... Thank you Regards Alessandro Mattozzi M.Phil., Ph.D. student Dept. of Fibre and Polymer Technology Royal Institute of Technology Stockholm, Sweden ___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Free volume: Pass and Gromacs
Title: Free volume: Pass and Gromacs Hi all I wonder if anybody has been using Pass to measure free volume: I got these errors: -Error: Found an odd element (B) on atom #13454. Hydrogen radius assigned. Suggestion: Do I have to remove all the dummies? -Segmentation fault Suggestion: I use trjconv to get a pdb; is it possible that I am doing some mistake in the conversion? Thanx Alessandro Mattozzi M.Phil., Ph.D. student Dept. of Fibre and Polymer Technology Royal Institute of Technology Stockholm, Sweden ___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Position restrain
While running a MD of PE with position restrain, i get this error message Fatal error: [ file posre.itp, line 6 ]: Atom index (101) in position_restraints out of bounds (1-12) My atom index goes up to 6000, why do I have to be in the 1-12 range? your molecule only has 12 atoms and by the way, the error message is from grompp. actually my molecule has 12 thousand atoms, half of it dummies and half AUA. The .gro and .ndx contains atoms numbered up to 12000 The error ideed comes from grompp. Thanx Regards Alessandro Mattozzi M.Phil., Ph.D. student Dept. of Fibre and Polymer Technology Royal Institute of Technology Stockholm, Sweden winmail.dat___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] FW: Position restrain
Title: FW: Position restrain Hi gmx-users While running a MD of PE with position restrain, i get this error message Fatal error: [ file posre.itp, line 6 ]: Atom index (101) in position_restraints out of bounds (1-12) My atom index goes up to 6000, why do I have to be in the 1-12 range? Regards Alessandro Mattozzi M.Phil., Ph.D. student Dept. of Fibre and Polymer Technology Royal Institute of Technology Stockholm, Sweden ___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Position restrain
Title: Position restrain While running a MD of PE with position restrain, i get this error message Fatal error: [ file posre.itp, line 6 ]: Atom index (101) in position_restraints out of bounds (1-12) My atom index goes up to 6000, why do I have to be in the 1-12 range? Regards Alessandro Mattozzi M.Phil., Ph.D. student Dept. of Fibre and Polymer Technology Royal Institute of Technology Stockholm, Sweden ___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Free Volume-Pass11
I tried to find it but did not suceed. Do you have tips? Thanx Alessandro Mattozzi M.Phil., Ph.D. student Dept. of Fibre and Polymer Technology Royal Institute of Technology Stockholm, Sweden -Original Message- From: [EMAIL PROTECTED] on behalf of David van der Spoel Sent: Wed 5/17/2006 11:58 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Free Volume Alessandro Mattozzi wrote: Hi All I was wondering if there is any built-in function for the calculation of free-volume distribution in a polymer system. Thanks a lot not really, but you could try to use the pass11 program (not gromacs), which places small balls in empty spaces and then count them. You are of course welcome to contribute a new analysis tool :) Regards Alessandro Mattozzi Dept. of Fibre and Polymer Technology Royal Institute of Technology Stockholm, Sweden Alessandro Mattozzi M.Phil., Ph.D. student Dept. of Fibre and Polymer Technology Royal Institute of Technology Stockholm, Sweden ___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] 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 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php winmail.dat___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
