Re: [gmx-users] intel compiler + amd64: help needed.

Jones de Andrade wrote: Hi all. Ok, I admit that I've posted it before. But I still not finding the error that makes the gromacs compilation with intel compilers not work on my AMD64 machine here. The error I get is still the following: **

[gmx-users] intel compiler + amd64: help needed.

Hi all. Ok, I admit that I've posted it before. But I still not finding the error that makes the gromacs compilation with intel compilers not work on my AMD64 machine here. The error I get is still the following: ** ./mk

[gmx-users] Warnings in runing tutorial files

Dear all,  I tried to run the tutorial examples. Although, for one of them (speptide) the process was implemented successfully, but, for the other examples (water, methanol and mixed) surprisingly I got the following error when I tried to execute grompp –v command:  --

Re: [gmx-users] Coordinates of the Centre of Mass.

hi..thank you. Got it. Annie AlbinOn 5/29/06, X.Periole <[EMAIL PROTECTED]> wrote: On Mon, 29 May 2006 12:14:04 +0530  "Annie Albin" <[EMAIL PROTECTED]> wrote:> Hi all,>>   I would like to know if there is a way by which we >can get to know> the coordinates of the centre of mass for the>molecul

RE: [gmx-users] step.pdb files with titel "one step before crash"

George, > I am trying to run mdrun. It always prompts the following message and > creates two pdb files stepN.pdb and #stepN.pdb.1# (where N is > the step > number) in each step. A stepN.pdb has a TITLE line "one step > before crash" > and #stepN-1.pdb.1 has a TITLE "crash". I'd like to know

Re: [gmx-users] Re: TI, sampling, sc_power, and sc_alpha

Matt, On 5/30/06, [EMAIL PROTECTED] <[EMAIL PROTECTED]> wrote: David, I forgot to ask: You said that " the soft core settings that work well for the vdW portion make the charging portion a more "difficult" transformation than normal, and the settings that work well for charging make the vdW p

Re: [gmx-users] Re: TI, sampling, sc_power, and sc_alpha

Matt, Re sc-power, you *do* want sc-power=1. I am not sure about defaults. David, when you talk of splitting the vdW and charge mutations into separate stages, you mean initially (for example) setting the B-states to have only altered atom types (and hence vdW radii), then later extending the

[gmx-users] Re: TI, sampling, sc_power, and sc_alpha

David, I forgot to ask: You said that " the soft core settings that work well for the vdW portion make the charging portion a more "difficult" transformation than normal, and the settings that work well for charging make the vdW portion "difficult". " What settings would you initially suggest t

[gmx-users] Re: TI, sampling, sc_power, and sc_alpha

David and Berk, I enormously appreciate your help in diagnosing my free energy problems. Berk, when you said "I had implemented the alpha=1 option in 3.3 and set it as default" I presume you mean the sc_power=1 option, yes? David, when you talk of splitting the vdW and charge mutations into sep

[gmx-users] step.pdb files with titel "one step before crash"

Dear all, I am trying to run mdrun. It always prompts the following message and creates two pdb files stepN.pdb and #stepN.pdb.1# (where N is the step number) in each step. A stepN.pdb has a TITLE line "one step before crash" and #stepN-1.pdb.1 has a TITLE "crash". I'd like to know what's wron

Re: [gmx-users] system size.

:) thanks a ton. -karamyog.On 5/30/06, Mark Abraham <[EMAIL PROTECTED]> wrote: karamyog singh wrote:> Is there any limit for the system size that i want to simulate in gromacs?No, you are limited by your hardware and your lifetime.Mark___ gmx-users mailin

Re: [gmx-users] system size.

karamyog singh wrote: Is there any limit for the system size that i want to simulate in gromacs? - karamyog. ___ gmx-users mailing listgmx-users@gromacs.org http://www.groma

Re: [gmx-users] system size.

karamyog singh wrote: Is there any limit for the system size that i want to simulate in gromacs? No, you are limited by your hardware and your lifetime. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/

[gmx-users] system size.

Is there any limit for the system size that i want to simulate in gromacs? - karamyog. ___ 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

[gmx-users] how choose k value in .ppa file

Hi, gromacs users I've a little question about the pulling procedure at constant rate. I defined pull and reference group both constituted by 18 atoms. My problem is to define the spring value in .ppa file. Given that my groups have N atoms, how do I choose a suitable spring value quantitative

Re: [gmx-users] Different gromacs version question

Anthony Cruz wrote: Hi: is possible to run a system that I prepared with the 3.2.1 version in the 3.3.1 without problems??? If not, it is a bug. Anthony ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gm

[gmx-users] Different gromacs version question

Hi: is possible to run a system that I prepared with the 3.2.1 version in the 3.3.1 without problems??? Anthony ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe request

Re: [gmx-users] Problem: parallel inefficient scaling with Mac Intel Core Duo

Yiannis Nicolis wrote: Le 29 mai 06 à 20:46, David van der Spoel a écrit : Yiannis wrote: Hello, Has anybody tried to use gromacs in parallel with the Intel Core Duo macintoshes? I installed gromacs and lam on some iMac with intel core duo 2x1.83GHz running the latest OSX with all updat

Re: [gmx-users] Problem: parallel inefficient scaling with Mac Intel Core Duo

Le 29 mai 06 à 20:46, David van der Spoel a écrit : Yiannis wrote: Hello, Has anybody tried to use gromacs in parallel with the Intel Core Duo macintoshes? I installed gromacs and lam on some iMac with intel core duo 2x1.83GHz running the latest OSX with all updates. I have everything wor

[gmx-users] How to use the simulated annealing porotocal of gromacs 3.3?

Dear all, I am trying to use the simulated annealing porotocal of gromacs 3.3 (single precision) to find the global energy minimization of a protein in a water box. I set the mdp file as follow: ; VARIOUS PREPROCESSING OPTIONS title= Simul