- Contemporary messages sorted: [ by date ] [ by thread ] [ by subject ] [ by author ] [ by messages with attachments ]

From: Vlad Cojocaru <Vlad.Cojocaru.mpi-bpc.mpg.de>

Date: Mon, 28 Jul 2003 15:58:55 +0200

Dear Amber users,

During a simulation with ntt=1 and tautp

the velocities are scaled proportionally per time step from v to lambda*v

where

lambda=1 + (delta)t/2*tautp(T0/T-1) and tautp (from the namelist is

taken in this equation by sander).

Please let me know if this is correct or not.

Trying to swich to NAMD

The equation given in the XPLOR program:

bi=biT(T0/T-1)

where bi is the friction coefficient applied by the program and biT is

the coefficient that we have to supply in tCoupleFile (please let me

know if this is correct ...this is just my thought)...so I fugured out

comparing the 2 eq. that:

biT=(delta)t/2*tautp where (delta)t is the timestep.

so for an equilibration in amber with (delta)t=0.001 and ntt=1 and tautp=0.2

I came up with a biT=0.0025 that has to be set in the tCoupleFile for

running a similar simulation using NAMD.

Please let me know if my assumptions were correct and if this makes

sense...I know it might be trash but somehow I need to run NAMD on The

cluster that I am using now because there is a problem with Amber and I

a have a "time pressure problem" and I am trying to use the same

protocol for the 2 programs.

Thanks a lot for understanding this,

Best wishes,

vlad

Date: Mon, 28 Jul 2003 15:58:55 +0200

Dear Amber users,

During a simulation with ntt=1 and tautp

the velocities are scaled proportionally per time step from v to lambda*v

where

lambda=1 + (delta)t/2*tautp(T0/T-1) and tautp (from the namelist is

taken in this equation by sander).

Please let me know if this is correct or not.

Trying to swich to NAMD

The equation given in the XPLOR program:

bi=biT(T0/T-1)

where bi is the friction coefficient applied by the program and biT is

the coefficient that we have to supply in tCoupleFile (please let me

know if this is correct ...this is just my thought)...so I fugured out

comparing the 2 eq. that:

biT=(delta)t/2*tautp where (delta)t is the timestep.

so for an equilibration in amber with (delta)t=0.001 and ntt=1 and tautp=0.2

I came up with a biT=0.0025 that has to be set in the tCoupleFile for

running a similar simulation using NAMD.

Please let me know if my assumptions were correct and if this makes

sense...I know it might be trash but somehow I need to run NAMD on The

cluster that I am using now because there is a problem with Amber and I

a have a "time pressure problem" and I am trying to use the same

protocol for the 2 programs.

Thanks a lot for understanding this,

Best wishes,

vlad

-- Vlad Cojocaru Max Planck Institute for Biophysical Chemistry Department: 060 Am Fassberg 11, 37077 Goettingen, Germany tel: ++49-551-201.1327 e-mail: Vlad.Cojocaru.mpi-bpc.mpg.de home tel: ++49-551-9963204 ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to amber.scripps.edu To unsubscribe, send "unsubscribe amber" to majordomo.scripps.eduReceived on Mon Jul 28 2003 - 15:53:01 PDT

Custom Search