From: harish vashisth (harish.vashisth_at_gmail.com)
Date: Tue Jun 12 2012 - 11:22:10 CDT
I think it would be very useful if you can spend sometime doing exercises
in the NAMD tutorial. Once you know how to successfully run those, refer to
the NAMD user's guide to add specific features to your config file...this
is something every new user does, i suppose..
On Tue, Jun 12, 2012 at 7:02 AM, Miguel Ángel Mompeán García <
mig.mompean_at_gmail.com> wrote:
> Dear NAMD users,
>
> I am very new with this program and I want to know how to properly set my
> conf file for a TMD work.
> I have minimized, and NVT and NPT-equilibrated both the two structures to
> be studied.
>
> Let say that I want to go from stateA.pdb to stateB.pdb Should I just
> indicate in the conf file
>
>
> ##ADJUSTABLE PARAMETERS
>
> structure $WORKING_DIRECTORY/stateA.psf
> coordinates $WORKING_DIRECTORY/stateA.pdb
> firsttimestep 0
>
>
>
> And then:
>
>
> ## EXTRA PARAMETERS
>
> TMD on
> TMDK 20
> TMDFile $WORKING_DIRECTORY/stateB.pdb
> TMDFirststep 0
>
>
> Or should I continue the simulation doing a restart from the NPT
> equilibration at the last point and include binCoordinates, binVelocities
> and binExtendedSystem?
>
> If so, I guess I should set up the TMDFile not just as the initial
> "stateB.pdb", but as the pdb resulting from the NPT equilibration. How can
> I extract those coordinates from the simulation?
>
>
> Thanks for your help.
>
> Best regards,
> Migue
>
>
>
>
>
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