[gmx-users] shell molecular dynamics

Hello, I would like to run a simulation using the shell option. I tried to restraint solvent molecules which were found within the range of 5-10 angstroms from the box center. I couldn't find any way to do so. I didn't find any information about this topic anywhere else i.e. GROMACS manual,

Re: [gmx-users] shell molecular dynamics

On 29/12/2011 9:43 PM, michael zhenin wrote: Hello, I would like to run a simulation using the shell option. I tried to restraint solvent molecules which were found within the range of 5-10 angstroms from the box center. I couldn't find any way to do so. I didn't find any

[gmx-users] shell molecular dynamics

Hi, all, I am doing shell molecular dynamics and I have read the sw.itp. Now my question is: 1. For the shell atom, what element should be used in .pdb file, since the 77-78th digits of pdb file is element symbol ? 2. What does the 1 in [ polarization ] part mean in sw.itp? 3. Is it

Re: [gmx-users] shell molecular dynamics

Shuangxing Dai wrote: Hi, all, I am doing shell molecular dynamics and I have read the sw.itp. Now my question is: 1. For the shell atom, what element should be used in .pdb file, since the 77-78th digits of pdb file is element symbol ? Anything you like. Gromacs does not use this

Re: [gmx-users] shell molecular dynamics

is the problem. Shuangxing Dai - Original Message - From: David van der Spoel sp...@xray.bmc.uu.se To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: 13 April, 2009 11:15 AM Subject: Re: [gmx-users] shell molecular dynamics Shuangxing Dai wrote: Hi, all, I am doing

Re: [gmx-users] shell molecular dynamics

far away from the core to get effective polarization. Shuangxing Dai - Original Message - From: David van der Spoel sp...@xray.bmc.uu.se To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: 13 April, 2009 11:15 AM Subject: Re: [gmx-users] shell molecular dynamics