On 5/18/13 1:23 AM, Shima Arasteh wrote:
If I skip the pulling code step, how could I generate configurations while
there are one ion in each window? Am I supposed to save my favorite snapshots
during MD simulation trajectory?
You can generate configurations in any way you see fit. SMD is
for GROMACS
users
Cc:
Sent: Friday, May 17, 2013 4:02 PM
Subject: Re: [gmx-users] Re: Running Pull Code
On 5/17/13 7:16 AM, Shima Arasteh wrote:
> Thanks for your reply.
> It' s around 5 nano seconds that I ran equilibration time on the system, and
> the average pressure I s
to go. See what many do, and base what you try off of
what you find.
-Justin
Sincerely,
Shima
- Original Message -
From: Justin Lemkul
To: Shima Arasteh ; Discussion list for GROMACS users
Cc:
Sent: Friday, May 17, 2013 4:02 PM
Subject: Re: [gmx-users] Re: Running Pull Code
On
17, 2013 4:02 PM
Subject: Re: [gmx-users] Re: Running Pull Code
On 5/17/13 7:16 AM, Shima Arasteh wrote:
> Thanks for your reply.
> It' s around 5 nano seconds that I ran equilibration time on the system, and
> the average pressure I see as a result, seems sensible. However I am
, 2013 4:02 PM
Subject: Re: [gmx-users] Re: Running Pull Code
On 5/17/13 7:16 AM, Shima Arasteh wrote:
> Thanks for your reply.
> It' s around 5 nano seconds that I ran equilibration time on the system, and
> the average pressure I see as a result, seems sensible. However I am
ppreciate your suggestion.
Sincerely,
Shima
- Original Message -
From: Thomas Schlesier
To: gmx-users@gromacs.org
Cc:
Sent: Friday, May 17, 2013 3:30 PM
Subject: [gmx-users] Re: Running Pull Code
The three steps (EM, NVT and NPT) are to equilibrate the system. How
much time these steps need d
ge of sufficient equilibration time.
I appreciate your suggestion.
Sincerely,
Shima
- Original Message -
From: Thomas Schlesier
To: gmx-users@gromacs.org
Cc:
Sent: Friday, May 17, 2013 3:30 PM
Subject: [gmx-users] Re: Running Pull Code
The three steps (EM, NVT and NPT) are to equili
The three steps (EM, NVT and NPT) are to equilibrate the system. How
much time these steps need depends on the system. But i would assume a
ouple of nanosecounds are sufficient for most systems. You could look
into the literature, how long other people equilibrate systems which are
similar to o
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