AMBER Archive (2009)

Subject: Re: [AMBER] Problem with REMD

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Thu Mar 12 2009 - 06:00:07 CDT

1) it is tremendously helpful to tell people what amber version you are
using. remd has changed very much between amber 9 and 10.
2) did the remd test cases pass on this machine?

On Thu, Mar 12, 2009 at 3:45 AM, parul sharma <sharmaparul7373_at_gmail.com>wrote:

> Dear All,
>
> I am trying to run REMD simulation on a dipeptide (6 replicas) using the
> input for one of the replica:
>
> &cntrl
> imin=0,
> ntc=2, ntf=2,
> cut=99, igb=5, saltcon=0.2, gbsa=1,
> ntpr=50, surften=0.005,
> nstlim=1000, dt=0.002, numexchg=1000,
> ntt=3, gamma_ln=1, temp0=586,
> ntx=5, irest=1, ntb=0,
> ntpr=500, ntwx=500, ntwr=500, ntwe=500, nscm=1000,
> &end
> The groupfile used looks like:
>
> #
> # replica
> #
> -A -i boxeq240.in -p di.prmtop -o boxeq240.out -c crd240-1to1000ps -r
> 240.rst -x crd240
> -A -i boxeq300.in -p di.prmtop -o boxeq300.out -c crd300-1to1000ps -r
> 300.rst -x crd300
> -A -i boxeq375.in -p di.prmtop -o boxeq375.out -c crd375-1to1000ps -r
> 375.rst -x crd375
> -A -i boxeq469.in -p di.prmtop -o boxeq469.out -c crd469-1to1000ps -r
> 469.rst -x crd469
> -A -i boxeq586.in -p di.prmtop -o boxeq586.out -c crd586-1to1000ps -r
> 586.rst -x crd586
> -A -i boxeq732.in -p di.prmtop -o boxeq732.out -c crd732-1to1000ps -r
> 732.rst -x crd732
>
> However, i am not able to find rem.log as the output, also the boxeq240.out
> is not showing any progress in the Atomic coordinates and velocities, and
> looks like below:
>
> 2. CONTROL DATA FOR THE RUN
>
> --------------------------------------------------------------------------------
> NGLY
> General flags:
> imin = 0, nmropt = 0
> Replica exchange
> numexchg= 1000
> Nature and format of input:
> ntx = 5, irest = 1, ntrx = 1
> Nature and format of output:
> ntxo = 1, ntpr = 500, ntrx = 1, ntwr =
> 500
> iwrap = 0, ntwx = 500, ntwv = 0, ntwe =
> 500
> ioutfm = 0, ntwprt = 0, idecomp = 0,
> rbornstat= 0
> Potential function:
> ntf = 2, ntb = 0, igb = 5, nsnb =
> 25
> ipol = 0, gbsa = 1, iesp = 0
> dielc = 1.00000, cut = 99.00000, intdiel = 1.00000
> saltcon = 0.20000, offset = 0.09000, gbalpha= 1.00000
> gbbeta = 0.80000, gbgamma = 4.85100, surften = 0.00500
> rdt = 0.00000, rgbmax = 25.00000
> alpb = 0
> scnb = 2.00000, scee = 1.20000
> Frozen or restrained atoms:
> ibelly = 0, ntr = 0
> Molecular dynamics:
> nstlim = 1000, nscm = 1000, nrespa = 1
> t = 0.00000, dt = 0.00200, vlimit = 20.00000
> Langevin dynamics temperature regulation:
> ig = 71277
> temp0 = 240.00000, tempi = 0.00000, gamma_ln= 1.00000
> SHAKE:
> ntc = 2, jfastw = 0
> tol = 0.00001
> | INFO: Old style inpcrd file read
>
>
> --------------------------------------------------------------------------------
> 3. ATOMIC COORDINATES AND VELOCITIES
>
> --------------------------------------------------------------------------------
>
> Please help me to sort out this problem.
>
> Thanks in Advance
>
> regards
> Parul Sharma
>
>
>
>
>
>
> --
> With Best Regards
>
> Parul Sharma
> PhD Student, Durban University of Technology,
> Durban,
> South Africa
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>
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