[gmx-users] Re: Running Pull Code

Justin Lemkul jalemkul at vt.edu
Sat May 18 04:10:25 CEST 2013

On 5/17/13 8:25 AM, Shima Arasteh wrote:
> Thanks for your reply.
> In fact, I plan to study ion conduction through the peptide inserted in lipid membrane and acting as an ion channel. According to the literature, an ion across the membrane in less than 20 ns.
> Can I decide upon this information to apply pull code?
> You simulated the protofibril structures for 100 ns, in another article 25 ns.
>   Ok, if there is not any universal recipe for it, what do you suggest me? Try and error?

Assess the literature thoroughly.  Basing your plan on only one paper may not be 
the most productive way to go.  See what many do, and base what you try off of 
what you find.


> Sincerely,
> Shima
> ----- Original Message -----
> From: Justin Lemkul <jalemkul at vt.edu>
> To: Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org>
> 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 see as a result, seems sensible. However I am not sure if this criteria is sufficient? Others suggest to evaluate the box-dimension changes using g_energy code to judge of sufficient equilibration time.
> The box vectors won't tell you anything more than the pressure will since
> they're related quantities.
> The better question is, "What is a suitable starting structure for the system of
> interest?"  The umbrella sampling tutorial (which everyone seems to take at
> literal face value as the only way to do things, which it is decidedly not)
> presents a simple, easy-to-understand method.  In the paper I did (upon which I
> based the tutorial), I simulated the protofibril structures for 100 ns before I
> was confident they were suitably stable and representative of viable structures
> for doing SMD and US.  Your mileage will vary and depends on the quality of the
> starting structure and what it is that you hope to determine.  There is no magic
> recipe that is universal.
> -Justin
>> I appreciate your suggestion.
>> Sincerely,
>> Shima
>> ----- Original Message -----
>> From: Thomas Schlesier <schlesi at uni-mainz.de>
>> To: gmx-users at 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 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 ours.
>> If the system is equilibrated, you an start to perform the pulling
>> simulation to obtain the individual structure for the later umbrella
>> sampling.
>> Greetings
>> Thomas
>> Am 17.05.2013 07:46, schrieb gmx-users-request at gromacs.org:
>>> Hi,
>>> I have a system composed of POPC/peptide/water/ions. I aim to study ion conduction through the peptide using umbrella sampling.
>>> I built the system and ran EM, NVT, NPT successfully, but have not run md yet. I' d like to know if the system is required of passing a few nanoseconds md? Or I might be able to go to Umbrella Sampling straight after NPT?
>>> As I studied in Justin's tutorial, running pull code is done after some typical steps of every simulation ( EM, NVT, NPT). But I dont know if is correct generally for other systems as well?
>>> Would you please give me any suggestions?
>>> Thanks in advance.
>>> Sincerely,
>>> Shima?


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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