Re: [gmx-users] How to calculate the local electric field?

Zhang Zhigang wrote: Hi, all, Is it possible to use an established program in Gromacs 4.0 package to analysis the distributions of the local electric fields? Let me explain the situation clearer as following: In a pure water system, each molecule would feel a local electric

[gmx-users] error while compiling gromacs 4.0.2

Dear all, While compiling gromacs 4.0.2 in a AMD 64bit dual processor system, I encounter the following error while configuring: checking size of int... configure: error: cannot compute sizeof (int) See `config.log' for more details. Please let me know where I have gone wrong. I am pasting the

[gmx-users] plz ignore my previous mail

Sorry..for sending an incomplete mail. Please ignore my previous mail. Raghu Add more friends to your messenger and enjoy! Go to http://messenger.yahoo.com/invite/ ___ gmx-users mailing listgmx-users@gromacs.org

[gmx-users] quad cpu

I searched the mailing list and I found some reports about low performance of intel core2 quad cpus in parallel mode I have the same problem and I see low cpu usage(intel core2 quad)in parallel run. do you have some solution or comment for this problem of intel quad cpus? thank you

Re: [gmx-users] quad cpu

ha salem wrote: I searched the mailing list and I found some reports about low performance of intel core2 quad cpus in parallel mode I have the same problem and I see low cpu usage(intel core2 quad)in parallel run. do you have some solution or comment for this problem of intel quad cpus? thank

[gmx-users] Selecting force field for simulation in vacuum

Hello everyone! I'm having some problems for selecting force field for a simulation in vacuum. I'm using version 4.0.2. According to pdb2gmx man page (pdb2gmx -h) DESCRIPTION --- This program reads a pdb file, reads some database files, adds hydrogens to

Re: [gmx-users] Selecting force field for simulation in vacuum

GROMOS and OPLS were derived for condensed-phase properties, so none of those will be useful. I know nothing about ENCAD, however, but I do not often see it in the literature. -Justin Nuno Azoia wrote: Hello everyone! I'm having some problems for selecting force field for a simulation in

RE: [gmx-users] Selecting force field for simulation in vacuum

Hi, It depends on what you mean with vacuum simulation. Do you mean really simulating how a protein would behave in vacuum? Or do you want some type of implicit solvent? OPLS has been parametrized on the properties of pure liquids of small compounds. For Gromos at least the liquid properties of

Re: [gmx-users] Re: Re: How to calculate the local electric field?

Zhang Zhigang wrote: Hi, Mark, Thanks for your reply. You mean g_potential in the program lists? It is related with electric field but can not give the local electric field, isn't it? That question is answered by the documentation for g_potential, which is also in the manual :-)

Re: [gmx-users] Selecting force field for simulation in vacuum

Justin A. Lemkul wrote: GROMOS and OPLS were derived for condensed-phase properties, so none of those will be useful. I know nothing about ENCAD, however, but I do not often see it in the literature. This depends on the kind of substance you are simulating. If polarization is relatively

RE: [gmx-users] Selecting force field for simulation in vacuum

Hi, Well, what I really need is a simulations without the solvent, because solvent calculations are time consuming, especially for water. What do you mean by implicit solvent? I check the mailing list and I have found some discussions about this, and I've found some papers that now I need to

RE: [gmx-users] Selecting force field for simulation in vacuum

Hi, There are no good general purpose implicit solvent force fields. But there are many around for specific purposes. In Gromacs 4.1 there will be generalized Born implicit solvent, but that will not be a lot faster than explicit water. Berk Subject: RE: [gmx-users] Selecting force field for

[gmx-users] work from pulling simulation

Hi, Thanks for the quick response, and I apologize for being too vague. Here's a second attempt. In Gromacs 3.3.1, I am running a steered MD simulation with commands, mdrun -s topol -o traj.trr -e ener -c conf -g log \ -pi pull.ppa -pn pull.ndx \ -pd pull.pdo -po pullout.ppa Here

Re: [gmx-users] error while compiling gromacs 4.0.2

try to add in your .bashrc this export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/openmpi-1.2.8/lib or whatever your mpi lib directory is Andrei On Thu, Dec 4, 2008 at 12:08 PM, Ragothaman Yennamalli [EMAIL PROTECTED] wrote: Dear all, While compiling gromacs 4.0.2 in a AMD 64bit dual

[gmx-users] work from pulling simulation

Quoting: So for the above sample data, at t = .002, I get F = Spring Force = AfmK * (18.042686- 18.042795) == AfmK * -0.000109 dZ = Change in Position of spring = (18.042795-18.042684) == 0.000111 Work by spring on Pulled group = F * dZ = AfmK * -0.000109 * 0.000111 ??? * I get

Re: [gmx-users] quad cpu

ha salem wrote: I have gromacs 4 and this problem still exist OK, can you be more specific in this case? If you run the benchmark like d.dppc you should get at least 90% scaling I would think. --- On Thu, 12/4/08, David van der Spoel [EMAIL PROTECTED] wrote: From: David van der Spoel

Re: [gmx-users] quad cpu

hello how I can run it?is it a gromacs command? --- On Thu, 12/4/08, David van der Spoel [EMAIL PROTECTED] wrote: From: David van der Spoel [EMAIL PROTECTED] Subject: Re: [gmx-users] quad cpu To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Thursday, December 4, 2008, 6:02

Re: [gmx-users] Force field selection

Lucio Montero wrote: Hello! What is the best force field to use for a MD of a compley of three proteins and an organic molecule. And what are the best temperature and pressure coupling methods. Best is completely subjective, based on what you read about different force fields and which

Re: [gmx-users] quad cpu

ha salem wrote: hello how I can run it?is it a gromacs command? No, you have to download a package of benchmark calculations and run them. Look on the GROMACS website. Mark ___ gmx-users mailing listgmx-users@gromacs.org

[gmx-users] time constants on distance restraints between three molecules

Hi, all, Thank you for you input with previous questions. I have have three molecules: A, B, and C. I have distance restraints between A and B, and B and C. I was wondering, if there is a way to put a different time constant for the distance restraint between A and B than B and C.

Re: [gmx-users] time constants on distance restraints between three molecules

Arthur Roberts wrote: Hi, all, Thank you for you input with previous questions. I have have three molecules: A, B, and C. I have distance restraints between A and B, and B and C. I was wondering, if there is a way to put a different time constant for the distance restraint between A and B

[gmx-users] help: how to set up a rigid system

2008-12-05 刘鑫 发件人： 刘鑫 发送时间： 2008-12-05 11:30:41 收件人： [EMAIL PROTECTED] 抄送： 主题： help: how to set up a rigid system Dear GMX users, I am carrying out MD simulation of acetylacetone by Gromacs. As we know, there are keto and enol two tautomers for acetylacetone. The tautomers were

[gmx-users] how to set up rigid system for acetylacetone

Dear GMX users, I am carrying out MD simulation of acetylacetone by Gromacs. As we know, there are keto and enol two tautomers for acetylacetone. The tautomers were treated as rigid species in the literature (Y.K. Park, C. H. Turner, J. Supercrit. Fluids 37 (2006) 201-208)). The parameters