Sir
I have looked into the rst file there are many *'s.
Firstly i took nstlim=2500000, dt=0.002.
as per ur suggestions i reduced the nstlim to 500000 with dt = 0.001, that also didnt worked out.i am still getting the *'s in the rst file. Now i have again run the simulations with nstlim=10000, dt=0.002.i am running the system in implicit solvent.
Please do suggest me.
With Regards
Priya Anand
Ross Walker <ross.rosswalker.co.uk> wrote:
Dear Priya,
Have you looked at the restart file to see if you can see what is wrong with it. Are there any *'s in the output file suggesting that your system drifted away from the original origin by too far? Have you visualized the trajectory? Does anything look wrong? Did your system blow up or did it remain stable?
Check if you set nscm to a reasonable value. If you are running this system in implicit solvent you probably need to set nscm=1000 or so to remove center of mass motion. Without doing this your system can drift a long way from the origin such that the coordinate values exceed the available space in the output and restart files.
Alternatively your restart file may have simply got corrupted due to hardware issues with your computer system. Without more details about the specific problem we can't help much more I am afraid.
All the best
Ross
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---------------------------------
From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of priya priya
Sent: Monday, August 21, 2006 00:46
To: amber.scripps.edu
Subject: AMBER: problem relating all atom structure prediction and folding simulations on AMBER8
Dear
I am doing the first stage of the simulation on 42 residue peptide at 325 K. Running 50 ns of simulation at 325 K in 10 stages of 5 ns each.
Input file reads as follows:
Stage 2 equilibration 1 0-5ns &cntrl imin=0, irest=1, ntx=5, nstlim=2500000, dt=0.002, ntc=2, ntf=2, ntt=1, tautp=0.5, tempi=325.0, temp0=325.0, ntpr=500, ntwx=500, ntb=0, igb=1, cut=999.,rgbmax=999. /
The commannd used for running simulation is
$AMBERHOME/exe/sander -O -i equil.in -p TC5b.prmtop -c heat7.rst -r equil1.rst -o equil1.out -x equil1.mdcrd
first step run well for 5 days but the rst file is not complete. when i run the next step of 5ns it gives an error as
forrtl: severe (64): input conversion error, unit 9, file /usr/local/amber8/exe/equil1.rst
so now i am unable to proceed further will be somebody guide me.
With Regards
Priya Anand
Department of Biophysics
Panjab University
Chandigarh.
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Received on Wed Aug 23 2006 - 06:07:19 PDT
