Re: Running Multiple TMD simultaneously

From: Jerome Henin (jhenin_at_cmm.chem.upenn.edu)
Date: Mon Sep 29 2008 - 11:34:14 CDT

Josh,
There is upcoming code in NAMD 2.7 that should give you lots of
freedom to perform that kind of biased simulations. It depends if you
can wait a little bit.
Jerome

On Sat, Sep 27, 2008 at 9:34 PM, Richard Law <drrichjlaw_at_gmail.com> wrote:
> Hey Josh,
> Either you could script it up with tcl forces or you could use constforce
> with a constforcefile which allows a separate vector for every atom.
> Rich.
>
> On Sat, Sep 27, 2008 at 12:57 PM, Joshua Adelman <jadelman_at_berkeley.edu>
> wrote:
>>
>> I was wondering if there was a straightforward way to rig namd to run two
>> TMD simulations simultaneously? I want to drive two different domains into
>> different conformations, but I don't want them to be correlated in any way.
>> In other words, I want to drive the two domains to particular conformations,
>> but I don't want the fitting of the two to be done together or relative to
>> one another.
>>
>> The simplest way to do this would be to just do TMD in two steps. You
>> could drive one domain to the desired conformation, and then drive the other
>> domain holding the first one restrained to the target position. This would
>> be sub-optimal since it would take twice as much simulation time.
>>
>> My previous experiences writing GlobalMaster-based source hacks of namd is
>> that you can't run two different GlobalMaster processes at the same time, so
>> I don't think I can just go in and duplicate the TMD code and just call it
>> something like TMD2 and then call them both in the config file.
>>
>> Any suggestions would be most appreciated.
>>
>> Josh
>>
>
>
>
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>
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