[gmx-users] RE:RE: How to calculate virial in gromacs-4.0? (xuji)

Hi Thank you for your explaination. But when I calculate the virial in all the inner force loops, the short range VDW and QQ force contribution to virial can be claculated straight forward. But when I claculate the bonded force, it seems difficult. Can you explain to me how to calculate the

[gmx-users] Amber port for GROMACS 4.0

Hi All, I was wondering how I can aquire AMBER ports for GROMACS4.0? Considering the ports given in (http://chemistry.csulb.edu/ffamber/) are suitable for version 3.3.3 and older. Noting the FAQ (http://chemistry.csulb.edu/ffamber/FAQ.html): - Can I use these ports with any version of GROMACS?

[gmx-users] gmx_bast subroutine error

Dear Gromacs Users, I have tried to start my job on 128 cores with 32 cores assigned for the PME calculation. I have got following error: --- Program mdrun, VERSION 4.0.2 Source code file: network.c, line: 357 Routine should not have been

Re: [gmx-users] gmx_bast subroutine error

Alexey Krukow wrote: Dear Gromacs Users, I have tried to start my job on 128 cores with 32 cores assigned for the PME calculation. I have got following error: --- Program mdrun, VERSION 4.0.2 Source code file: network.c, line: 357 Routine

RE: [gmx-users] gmx_bast subroutine error

If you mean Gromacs compilation, I am almost sure, that it is compiled with mpi support, but I have to ask our admins one more time. Thanks for your help. Best. -- Sensationsangebot verlängert: GMX FreeDSL - Telefonanschluss + DSL für nur 16,37 Euro/mtl.!*

[gmx-users] Freezing Groups

Hi everybody, I want to do a simulation using frozen groups and it seems it is much more difficult than I first thought. I searched the mailing list and I still have problems that I can't figure out. It is much appreciated if help me with these problems or point me in the right direction. The

[gmx-users] Accessing the distance_restraints energy term

Thanks Mark for your assistance. I have discovered the source of my problems in getting distance_restraints working. Without disre=simple in the mdp file, disre=no is assumed and, according to the manual: no distance restraints (ignore distance restraint information in topology file) While

Re: [gmx-users] Accessing the distance_restraints energy term

Chris Neale wrote: Thanks Mark for your assistance. I have discovered the source of my problems in getting distance_restraints working. Without disre=simple in the mdp file, disre=no is assumed and, according to the manual: no distance restraints (ignore distance restraint information in

Re: [gmx-users] Freezing Groups

Reza Salari wrote: Hi everybody, I want to do a simulation using frozen groups and it seems it is much more difficult than I first thought. I searched the mailing list and I still have problems that I can't figure out. It is much appreciated if help me with these problems or point me in the

Re: [gmx-users] Freezing Groups

Thank you very much Mark for your response. OK, if the [exclusions] way seems reasonable, I'll write the script and test it. I am also curious about knowing something. The manual says that When all non-bonded interactions within or between groups of atoms need to be excluded, is it more

[gmx-users] About REMD specification in mdrun argument

Hi, everyone! There's something that I'm not clear about REMD in gromacs. Since all the inputs are unified into a unique .tpr file, why should the REMD options -multi and -replex be sprcified as mdrun arguments instead of being integrated into the same .tpr file? -- Sun Li Department of Physics

Re: [gmx-users] About REMD specification in mdrun argument

Lee Soin wrote: Hi, everyone! There's something that I'm not clear about REMD in gromacs. Since all the inputs are unified into a unique .tpr file, why should the REMD options -multi and -replex be sprcified as mdrun arguments instead of being integrated into the same .tpr file? REMD is a

Re: [gmx-users] About REMD specification in mdrun argument

each tpr contains only one temperature. On Tue, Dec 2, 2008 at 1:29 PM, Lee Soin [EMAIL PROTECTED] wrote: Hi, everyone! There's something that I'm not clear about REMD in gromacs. Since all the inputs are unified into a unique .tpr file, why should the REMD options -multi and -replex be

[gmx-users] Segmentation fault during Simulated annealing for different groups

Hi All, I am trying to run simulated annealing for my protein + NDP kept in a water box. I want to vary the temperature for the NDP only and want to keep the constant temperature for rest of the system. for the same when tried with making two groups, one for NDP and other for rest of the

Re: [gmx-users] About REMD specification in mdrun argument

For some of the cases, all the .tpr files contain the same information except the coupling temperature. Isn't it elegant to add one more option for the specification of a list of temperatures for REMD simulation and incorporate all the information into a unique .tpr file? 2008/12/2 Yang Ye [EMAIL