[gmx-users] About the mdp file when doing umbrella samping simulation

Hi, Gromacs users, I am reading the portion of umbrella sampling in the Gromacs manu. I notice that noting is mentioned about the mdp file when doing umbrella sampling. Does it mean that we can use the normal mdp file as used in standard MD simulations to do umbrella sampling, together with ppa

[gmx-users] GromacsGUI 0.5.2 is available.

Dear GROMACS users, As you may know, GromacsGUI is a simple GUI for GROMACS which provide a working desk for it. I have tried to provide tools that one may need when working with GROMACS, all in one place: file management, file editing, interfaces for commands, xvg viewer, mdp editor and manual vi

Re: [gmx-users] Problems with GROMPP

Quoting Jens Pohl <[EMAIL PROTECTED]>: > > > -Ursprüngliche Nachricht- > > Von: Discussion list for GROMACS users > > Gesendet: 12.01.08 03:29:49 > > An: Discussion list for GROMACS users > > Betreff: Re: [gmx-users] Problems with GROMPP > > > > > > > > > It seems, that my protein is tru

Re: [gmx-users] Problems with GROMPP

Jens Pohl wrote: -Ursprüngliche Nachricht- Von: Discussion list for GROMACS users Gesendet: 12.01.08 03:29:49 An: Discussion list for GROMACS users Betreff: Re: [gmx-users] Problems with GROMPP It seems, that my protein is truncated in the xxx.gro file. The number of water molecu

Re: [gmx-users] Problems with GROMPP

> -Ursprüngliche Nachricht- > Von: Discussion list for GROMACS users > Gesendet: 12.01.08 03:29:49 > An: Discussion list for GROMACS users > Betreff: Re: [gmx-users] Problems with GROMPP > > > > It seems, that my protein is truncated in the xxx.gro file. The number of > > water mole

Re: [gmx-users] [Fwd: lipid simulation at low temperature (please help me to transmit the letter )]

Yang Ye wrote: > posting for my friend as her network has some problem. > > Dear gmx-users, I want to simulate lipid bilayers at temperature as low as > 230K, will the water near the head group of lipid freeze? If I want to get a > knowledge of the phase of lipid at temperature much lower t

Re: [gmx-users] Zdock

Siavoush Dastmalchi wrote: Hi There, I know this is not related to GMX, but was wondering if any one has any experience with mpi enabled zdock on linux based cluster. Specifically, I am trying to use zdock2.3_linux_mpi version on a cluster of Opteron 2212 CPUs. It looks like the application wor

[gmx-users] [Fwd: lipid simulation at low temperature (please help me to transmit the letter )]

posting for my friend as her network has some problem. Dear gmx-users, I want to simulate lipid bilayers at temperature as low as 230K, will the water near the head group of lipid freeze? If I want to get a knowledge of the phase of lipid at temperature much lower than zero, what should I

[gmx-users] Zdock

Hi There, I know this is not related to GMX, but was wondering if any one has any experience with mpi enabled zdock on linux based cluster. Specifically, I am trying to use zdock2.3_linux_mpi version on a cluster of Opteron 2212 CPUs. It looks like the application works on all nods but can not