Re: [gmx-users] how to interpretate a tpr file

Dongsheng Zhang wrote: Yang Ye, Thank you very much for your help. I still have some questions: On Mon, 2006-07-10 at 11:35 +0800, Yang Ye wrote: Dongsheng Zhang wrote: Dear GMX users: Could someone help me to understand these information from a position restrained tpr file? 1. e

Re: [gmx-users] minimum number of atoms required.

karamyog singh wrote: Dear users, I have a system with just one atom. I am using periodic boundary conditions. No matter what conditions I use, the atom doesnt seem to move. Are a minimum of 2 atoms required to do a simulation in Gromacs? If I have only one atom and I am using periodic boundary

Re: [gmx-users] how to interpretate a tpr file

Yang Ye, Thank you very much for your help. I still have some questions: On Mon, 2006-07-10 at 11:35 +0800, Yang Ye wrote: > Dongsheng Zhang wrote: > > Dear GMX users: > > > > > > Could someone help me to understand these information from a position > > restrained tpr file? > > > > 1. excl[0][0

Re: [gmx-users] setting up a random system

On Mon, 10 Jul 2006 15:13:19 +1200 "erwin berthier" <[EMAIL PROTECTED]> wrote: Hello Mark and Jay, Thanks for your advice. I see that if I start a system quite less dense and let it equilibrate during the run it avoids a lot of problems. If I don't do that even the energy minimisation process

Re: [gmx-users] how to interpretate a tpr file

Dongsheng Zhang wrote: Dear GMX users: Could someone help me to understand these information from a position restrained tpr file? 1. excl[0][0..17]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 13, 14, 15, 16, 18, 26, 28} Exclusion group 0, there are total 17 exclusions in

RE: [gmx-users] setting up a random system

> About that pressure scaling problem what is the importance of > tau_p? What does it mean if I change it from 1 to 100 for example? Coupling constant. See equation 3.29 in manual 1 to 100 will mean that the pressure will scale 100 times slower. Lower the number, faster the response and adjust

[gmx-users] setting up a random system

Hello Mark and Jay, Thanks for your advice. I see that if I start a system quite less dense and let it equilibrate during the run it avoids a lot of problems. If I don't do that even the energy minimisation process fails. But that seems to work now. I thought about removing some particles by hand

Re: [gmx-users] minimum number of atoms required.

have you used gen_vel=yes. Yang Ye karamyog singh wrote: Dear users, I have a system with just one atom. I am using periodic boundary conditions. No matter what conditions I use, the atom doesnt seem to move. Are a minimum of 2 atoms required to do a simulation in Gromacs? If I have only one

[gmx-users] export hydrogen bond indices per timestep

Hello, Does anyone know which lines need to be changed in the gmx_hbond.c code to determine which donor-hydrogen-acceptor indices exist at each timestep? In other words, I would like to export lines 1483 to 1505 (see below) for every timeslice where a hydrogen bond is located (lines 2069 to 2073)

[gmx-users] use both LJ and buckingham potential for nonbonded potential

Dear gmx users, I find a force field that uses both LJ and Buckingham potential for different nonbonded potentials. I would like to use it in gromacs. I have try it, gromacs gave me a fatal error: ERROR 1 [file "ffpolymernb.itp", line 49]: Trying to add Buck.ham (SR) while the default nonbond ty

[gmx-users] how to interpretate a tpr file

Dear GMX users: Could someone help me to understand these information from a position restrained tpr file? 1. excl[0][0..17]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 13, 14, 15, 16, 18, 26, 28} 2. blocks[CGS][0][0..19]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11,

[gmx-users] minimum number of atoms required.

Dear users, I have a system with just one atom. I am using periodic boundary conditions. No matter what conditions I use, the atom doesnt seem to move. Are a minimum of 2 atoms required to do a simulation in Gromacs? If I have only one atom and I am using periodic boundary conditions then whether I

Re: [gmx-users] Setting up a random system

On Sun, 9 Jul 2006, Mark Abraham wrote: Hello, I am trying to reproduce the assembly of phospholipids into a micel and so I fill a box using the genbox command. And then I solvate it using the same command. I have tried really hard to have it running but I get a segmentation fault at worst and at

Re: [gmx-users] mdrun vs mdrun_mpi

> I am puzzled by the exact differences between MPI runs of gromacs > using the mdrun and mdrun_mpi binaries. One will run calculations in parallel, the other will not :-) > For example, I can use... > > grompp -np 1 ... > mpirun n0 -c 2 mdrun ... > > To run a MD simulation on a single node w

[gmx-users] mdrun vs mdrun_mpi

I am puzzled by the exact differences between MPI runs of gromacs using the mdrun and mdrun_mpi binaries. For example, I can use... grompp -np 1 ... mpirun n0 -c 2 mdrun ... To run a MD simulation on a single node with two processors. Both cpus appear to be fully utilized. What I don't unders

Re: [gmx-users] Setting up a random system

> Hello, > I am trying to reproduce the assembly of phospholipids into a micel > and so I fill a box using the genbox command. And then I solvate it > using the same command. > I have tried really hard to have it running but I get a segmentation > fault at worst and at best a pressure scalling warn

[gmx-users] Setting up a random system

Hello, I am trying to reproduce the assembly of phospholipids into a micel and so I fill a box using the genbox command. And then I solvate it using the same command. I have tried really hard to have it running but I get a segmentation fault at worst and at best a pressure scalling warning after a

Re: [gmx-users] nonbond_params

On Sat, 8 Jul 2006, ARGYRIOS KARATRANTOS wrote: >HI Gromacs users, > >my question is if i have to denote under the [nonbond_params] same non bonded >atoms in a polymeric chain, such as C-C nonbonded interactions. > >i am giving the lennard jones parameters in the [atomtypes] for carbon(C). > >do