From: Wang Yi (dexterwy_at_gmail.com)
Date: Wed Aug 29 2012 - 10:05:44 CDT
check this out:
http://www.ks.uiuc.edu/Research/namd/2.9/ug/node55.html#SECTION000132400000000000000
all ColVar's in NAMD can take the atom groups defined in ways described in this page
___________________________
Yi (Yves) Wang
Duke University
On 2012-8-29, at 上午10:58, snoze pa wrote:
> Hi Yi,
> Do you have any sample script to do that.
> Thanks in advance.
> S
>
> On Mon, Aug 27, 2012 at 2:40 PM, Wang Yi <dexterwy_at_gmail.com> wrote:
> Use the Collective Variable function of NAMD. And in the atom selection entry, include the entire domain in the selection, so that you're pulling the CoM of that domain.
> ___________________________
>
> Yi (Yves) Wang
> Duke University
>
>
>
>
>
> On 2012-8-27, at 下午3:36, snoze pa wrote:
>
>> Dear NAMD users,
>>
>>
>> I am working on a multi domain protein. Protein domains are similar to immunoglobin but instead of pulling one residue( i.e applying pulling force at one residue) i want to pull one complete domain. Is it possible using SMD in NAMD? So far I am trying following protocol:
>>
>> 1. Calculate center of mass (CM) of a domain of interest and then pull the CM in desired direction.
>>
>> Is this approach is correct?
>>
>> Thank you very much for your attention.
>>
>> S
>>
>>
>
>
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