[gmx-users] How to recenter solvent around solute

Hello, I have performed simulations of protein+ligands (solute) in truncated octahedral unit cell of waters (solvent). I would like to retain the shape of unit cell and have the solute centered in such a way as to be completely surrounded by solvent. At this point, I cannot achieve this although

Re: [gmx-users] How to recenter solvent around solute

On Sat, May 7, 2011 at 11:02 AM, Justin A. Lemkul jalem...@vt.edu wrote: Dimitar Pachov wrote: Hello, I have performed simulations of protein+ligands (solute) in truncated octahedral unit cell of waters (solvent). I would like to retain the shape of unit cell and have the solute centered

Re: [gmx-users] How to recenter solvent around solute

Hi, On Sat, May 7, 2011 at 9:45 PM, Justin A. Lemkul jalem...@vt.edu wrote: Please clarify - do you wish to maintain the original triclinic representation (as -ur tric does) or do you wish to see the octahedral representation (as -pbc mol -ur compact gives)? My answer was based on your

[gmx-users] Why does the -append option exist?

At first, I thought the -append option of the mdrun command was great. However, I don't think it is anymore and have actually started questioning myself why it exists at the first place, and second, why has it become the default option in the newest versions? It is useless unless you run your

Re: [gmx-users] Why does the -append option exist?

:26 AM, Dimitar Pachov wrote If this is true, then it wants fixing, and fast, and will get it :-) However, it would be surprising for such a problem to exist and not have been reported up to now. This feature has been in the code for a year now, and while some minor issues have been fixed since

Re: [gmx-users] Why does the -append option exist?

On Sat, Jun 4, 2011 at 9:09 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 5/06/2011 3:11 AM, Dimitar Pachov wrote: On Fri, Jun 3, 2011 at 9:24 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 4/06/2011 8:26 AM, Dimitar Pachov wrote Here is an example

Re: [gmx-users] Why does the -append option exist?

On Sun, Jun 5, 2011 at 2:14 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 5/06/2011 12:31 PM, Dimitar Pachov wrote: As I said, the queue is like this: you submit the job, it finds an empty node, it goes there, however seconds later another user with higher privileges on that particular

Re: [gmx-users] Why does the -append option exist?

Hello, Just a quick update after a few shorts tests we (my colleague and I) quickly did. First, using *You can emulate this yourself by calling sleep 10s before mdrun and see if that's long enough to solve the latency issue in your case.* doesn't work for a few reasons, mainly because it

Re: [gmx-users] Why does the -append option exist?

you would get. Hope that helps a bit. Thanks, Dimitar Sander On Jun 7, 2011, at 23:21 , Dimitar Pachov wrote: Hello, Just a quick update after a few shorts tests we (my colleague and I) quickly did. First, using *You can emulate this yourself by calling sleep 10s before mdrun

Re: [gmx-users] Why does the -append option exist?

node or on the compute node? I did the test on the debug queue, so it was a compute node. Let me know if you need more info. Best, Dimitar Thanks Roland On Wed, Jun 8, 2011 at 1:17 PM, Dimitar Pachov dpac...@brandeis.eduwrote: Hello, On Wed, Jun 8, 2011 at 4:21 AM, Sander Pronk pr