[gmx-users] 3.3.2 Error when using the mpi option

Hi, I am trying to compile version 3.3.2 in the parallel mode. I use the following options to configure: ./configure --prefix=dir --disable-float -enable-mpi and receive the following error message: checking size of int... configure: error: cannot compute sizeof (int) Note: The non

RE: [gmx-users] Adding two peptides in a water box

Hi Guys, Thank very much for your time trying to help me with this issue. It seems from all your answers that adding two identical peptides, separated by a certain distance from each other, and then put them into a water box with ions is a simple task. However, it is still puzzling me.

[gmx-users] Adding two peptides in a water box

Hi Everybory, I would like to simulate the interaction between two separated peptides in a water box. Every peptide needs to be N-and C-terminated. I have tried different alternatives in order to create the corresponding GROMACS files to start my simulation. I have used the GROMACS porograms

RE: [gmx-users] grompp error

*? Cheers, Tsjerk On 4/23/07, Triguero, Luciano O [EMAIL PROTECTED] wrote: Hi Everybody, I have been working with the topolgy file creating a new residue type to include some metal-aminoacids ligand complex. So far, pdb2gmx provide the topology file without errors and this file seems

[gmx-users] grompp error

Hi Everybody, I have been working with the topolgy file creating a new residue type to include some metal-aminoacids ligand complex. So far, pdb2gmx provide the topology file without errors and this file seems to contain all te interaction I added in the correspondign databases. However, the

RE: [gmx-users] Running GROMACS in PBS

for GROMACS users Subject: Re: [gmx-users] Running GROMACS in PBS Triguero, Luciano O wrote: Hello Everyone, I have a small problem here and need your help. Let start telling that I had spend some time trying to solve the problem with the recommendations I found in the internet, however my

RE: [gmx-users] topology doesnt match

Check if you have all group types in your mdp file. Ciao, Luciano Dr. Luciano Triguero College of Art and Science Department of Physics and Chemistry Cox Science Building 1301 Memorial Drive, Room 146 P.O Box 249118 Coral Gables, FL 33124-0431 Cellular: 305-904-2419 Office:

[gmx-users] Running GROMACS in PBS

Hello Everyone, I have a small problem here and need your help. Let start telling that I had spend some time trying to solve the problem with the recommendations I found in the internet, however my problem persist. I am running gromacs in a cluster and want to use one single machine with 4

RE: [gmx-users] Restarting a gromacs calcluation

for which you have positions, velocities and energies? Tsjerk On 3/17/07, Triguero, Luciano O [EMAIL PROTECTED] wrote: Dear Users, Thank for your help. I started a 10 ns simulation, but it dies because of an error in the cluster PBS system, so I want to continue the simulation from the last (r,v

RE: [gmx-users] Restarting a gromacs calcluation

for GROMACS users Subject: Re: [gmx-users] Restarting a gromacs calcluation Can you be more specific? Continue or start new simulation. Use tpbconv to extend your simulation. On 3/16/2007 9:37 AM, Triguero, Luciano O wrote: Dear users, How do I restart a gromacs simulation? Ciao

RE: [gmx-users] Restarting a gromacs calcluation

of Yang Ye Sent: Fri 3/16/2007 8:49 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Restarting a gromacs calcluation Can you be more specific? Continue or start new simulation. Use tpbconv to extend your simulation. On 3/16/2007 9:37 AM, Triguero, Luciano O wrote: Dear users

[gmx-users] Charges?

Hi gromacs guru! Does any know a clever way on how to convert QM charges to group charges as in shown in the residue topology file? Ciao, Luciano Dr. Luciano Triguero College of Art and Science Department of Chemistry Cox Science Building 1301 Memorial Drive, Room 146 P.O Box 249118 Coral

[gmx-users] Advices needed!

Hello everyone, Does anyone in the list know how to overcome this problem? Error message after 2010 iter in mdrun simulation Warning: 1-4 interaction between 278 and 281 at distance 1.863 which is larger than the 1-4

[gmx-users] Advices needed!

146 P.O Box 249118 Coral Gables, FL 33124-0431 Cellular: 305-904-2419 Office: 305-284-3938 -Original Message- From: [EMAIL PROTECTED] on behalf of [EMAIL PROTECTED] Sent: Fri 2/23/2007 4:20 PM To: Triguero, Luciano O Subject: confirm b8025838efdf752ad8c0a2373dbf6dc10021d426 Mailing list

RE: [gmx-users] Advices needed!

2/23/2007 4:42 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Advices needed! Triguero, Luciano O wrote: Hi Everyone, I need your help in the following matter. How do I generate a .gro file from a pdb file where I added an oxygen atom to one of the residue? I get