Re: [gmx-users] writing trajectory with water molecules within a distance from protein

An update on this. I got the following to work: 1. use a vmd script closest.tcl (available on the vmd pages) to select closest N waters, and write a pdb file for each frame. 2. however, the above pdb files have different residue numbers for the water molecules for each frame because it is not the

Re: [gmx-users] writing trajectory with water molecules within a distance from protein

A work around will be available in the future as a plugin for VMD. For your reference read these threads: http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/14140.html http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/13217.html On 10 May 2011 03:12, Roland Schulz wrote: > > > O

Re: [gmx-users] writing trajectory with water molecules within a distance from protein

On Mon, May 9, 2011 at 6:28 PM, Mark Abraham wrote: > On 10/05/2011 12:50 AM, maria goranovic wrote: > >> Dear experts >> >> I have a protein simulation in a water box. I now want to write a >> trajectory containing only the protein, and water molecules within 5 >> Angstroms of the protein, with t

Re: [gmx-users] writing trajectory with water molecules within a distance from protein

You can use g_order for that with just a bit of additional scripting. Erik maria goranovic skrev 2011-05-10 09.17: So, one can probably do this using a simple script? for each frame make index file of water molecules within 0.5 nm using g_select extract frame based on above selection done co

Re: [gmx-users] writing trajectory with water molecules within a distance from protein

So, one can probably do this using a simple script? for each frame make index file of water molecules within 0.5 nm using g_select extract frame based on above selection done concatenate frames The only problem with the above would be that the number of water molecules selected might change wit

Re: [gmx-users] writing trajectory with water molecules within a distance from protein

On 10/05/2011 12:50 AM, maria goranovic wrote: Dear experts I have a protein simulation in a water box. I now want to write a trajectory containing only the protein, and water molecules within 5 Angstroms of the protein, with the water list being updated each time step. How can one do this? A

Re: [gmx-users] writing trajectory with water molecules within a distance from protein

Hi, there is no tool to do that. Trajectories assume to have the same number of atoms per frame. What you can do is use g_order (it gives you the water sorted by distance and the number of water within .5nm) or g_select (it can give you an index file with the atoms within .5nm for each frame) Rol

[gmx-users] writing trajectory with water molecules within a distance from protein

Dear experts I have a protein simulation in a water box. I now want to write a trajectory containing only the protein, and water molecules within 5 Angstroms of the protein, with the water list being updated each time step. How can one do this? Appreciate the help -- Maria G. Technical Universit