Re: [gmx-users] box size changed

2007-03-01 Thread Tsjerk Wassenaar
t; and a warning in the log file as > " the box size exploding". > > Very grateful for your advice and help!!! > > Nancy > > > > > - Original Message - From: "Mark Abraham" > <[EMAIL PROTECTED]> > To: "Discussion list for GROMACS use

Re: [gmx-users] box size changed

2007-03-01 Thread Erik Marklund
a warning in the log file as " the box size exploding". Very grateful for your advice and help!!! Nancy - Original Message - From: "Mark Abraham" <[EMAIL PROTECTED]> To: "Discussion list for GROMACS users" Sent: Wednesday, February 28, 2007 5:1

Re: [gmx-users] box size changed

2007-03-01 Thread Nancy Deng
ot;. Very grateful for your advice and help!!! Nancy - Original Message - From: "Mark Abraham" <[EMAIL PROTECTED]> To: "Discussion list for GROMACS users" Sent: Wednesday, February 28, 2007 5:15 PM Subject: Re: [gmx-users] box size changed Nancy Deng w

Re: [gmx-users] box size changed

2007-03-01 Thread Tsjerk Wassenaar
Nancy, My guess is that you have pressure coupling on. Now, what is the characteristic of vacuum? What will happen if you have a balloon filled with vacuum (and one small red car of almost negligible size) and you couple it to a reference pressure (keep it out in the air)? In the other case,

Re: [gmx-users] box size changed

2007-02-28 Thread Mark Abraham
Nancy Deng wrote: Hi Mark, Thanks for the quick response and the funny story :) I indeed want to collect the possible comformation of a certain small molecule (a little car made of 35 atoms around 15 A in length) by MD. Since obvious to my understanding that in vacume or in water environment

Re: [gmx-users] box size changed

2007-02-28 Thread Nancy Deng
age - From: "Mark Abraham" <[EMAIL PROTECTED]> To: "Discussion list for GROMACS users" Sent: Wednesday, February 28, 2007 3:42 PM Subject: Re: [gmx-users] box size changed Nancy Deng wrote: Dear All, I am a very beginner of Gromacs and currently trying to run t

Re: [gmx-users] box size changed

2007-02-28 Thread Mark Abraham
Nancy Deng wrote: Dear All, I am a very beginner of Gromacs and currently trying to run two small molecule (35 atoms) MD studies, one with water and the other without water (skip the "genbox" step). Surprisingly, the box size of the system containing only small molecule (without water) kept

[gmx-users] box size changed

2007-02-28 Thread Nancy Deng
Dear All, I am a very beginner of Gromacs and currently trying to run two small molecule (35 atoms) MD studies, one with water and the other without water (skip the "genbox" step). Surprisingly, the box size of the system containing only small molecule (without water) kept shrink till the pr