From: Wang Yi (dexterwy_at_gmail.com)
Date: Mon Mar 19 2012 - 13:09:42 CDT
Hi Johan,
Would you mind elaborating a bit more on the topic of Galilean invariance?
In Dr. Schulten's original paper on NPT ensembles of SMD, I didn't see the Galilean invariance explicitly mentioned.
Thanks~
___________________________
Yi (Yves) Wang
Duke University
On 2012-3-19, at 下午12:28, johan strumpfer wrote:
> Raghav,
>
> Namd can do this, but you should be careful of which thermostat you
> use. The Langevin thermostat is not Galilean invariant, so you should
> not use it when doing SMD. To get around this you should use the
> Lowe-Andersen thermostat which is Galilean invariant. In practice I've
> also found that NVT to give more reliable results than NPT.
>
> Cheers,
> Johan
>
> ------------------------------------------------------------------------------------------------------
> Johan Strumpfer: johanstr_at_ks.uiuc.edu www.ks.uiuc.edu/~johanstr
> Ph.D. Candidate
> Theoretical and Computational Biophysics Group
> 3115 Beckman Institute
> University of Illinois at Urbana-Champaign
> 405 N. Mathews
> Urbana, IL 61801, USA
> ------------------------------------------------------------------------------------------------------
>
>
>
> On Mon, Mar 19, 2012 at 11:20 AM, Wang Yi <dexterwy_at_gmail.com> wrote:
>> There are instructions on how to do SMD in NAMD, using either the
>> configuration file or the latest ColVar technique.
>>
>> You can find them in the NAMD manual online.
>> ___________________________
>>
>> Yi (Yves) Wang
>> Duke University
>>
>>
>>
>>
>>
>> On 2012-3-19, at 上午11:12, raghav singh wrote:
>>
>> Hello All,
>>
>> I wanted to know about SMD simulation using NPT ensemble...
>> NAMD has this freedom or not... any suggested article would be off great
>> help.
>>
>> Thank You all
>>
>> regrads
>> Raghav
>>
>>
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