[AMBER] how to run PIMD

From: Sangita Kachhap <sangita.imtech.res.in>
Date: Fri, 11 Mar 2011 22:59:20 +0530 (IST)

Hello all

I want to know about how to run Path Integral Molecular Dynamics Simulation.
When I checked amber11/test/PIMD/full_pimd_ntp_water
as suggested in manual there is a file: gf_pimd_ntp

-O -i pimd_ntp.in -p spcfw.top -c spcfw.rst.1 -o bead1.out -r bead1.rst -x
bead1.mdcrd -inf bead1.mdinfo -pimdout pimd_ntp.out
-O -i pimd_ntp.in -p spcfw.top -c spcfw.rst.2 -o bead2.out -r bead2.rst -x
bead2.mdcrd -inf bead2.mdinfo -pimdout pimd_ntp.out
-O -i pimd_ntp.in -p spcfw.top -c spcfw.rst.3 -o bead3.out -r bead3.rst -x
bead3.mdcrd -inf bead3.mdinfo -pimdout pimd_ntp.out
-O -i pimd_ntp.in -p spcfw.top -c spcfw.rst.4 -o bead4.out -r bead4.rst -x
bead4.mdcrd -inf bead4.mdinfo -pimdout pimd_ntp.out

I want to know how this file will be generate?

As in case Replica Exchange Molecular Dynamics Simulation same type of file is
used to REMD and which is generated by a script provided in tutorial.

With regard

Sangita Kachhap

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Received on Fri Mar 11 2011 - 09:30:13 PST
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