Hi,
Unless you have a specific reason, you really should be using NetCDF
restart files (ntxo=2), not ASCII restart files (ntxo=1). However, it
is very unusual for so many of the coordinate in an ASCII restart to
overflow, so definitely follow the advice to check your structure and
energies to make sure things aren't blowing up.
-Dan
On Tue, Jun 22, 2021 at 3:37 PM GALLO FACUNDO NAHUEL
<fgallo.cibion.conicet.gov.ar> wrote:
>
> Hi! I'm having trouble when running a ligand-protein MD simulation. For one specific ligand, when I run the first equilibration (eqv) the .rst7 coordinate file is nonsense. The same .mdin equilibration file works for all the other ligands in the same system, and the coordinates in the .rst7 files are correctly written, so it seems to be something wrong with the ligand.
> The .mdin used is:
>
>
> &cntrl
> IMIN=0,NMROPT=0,
> NTX=1,IREST=0,
> NTWR=100000,NTPR=20000,NTWX=20000,NTWV=0,NTWE=0,IWRAP=0,IOUTFM=1,NTXO=1,
> NTR=1,RESTRAINT_WT=50.0,RESTRAINTMASK=':1-633',
> MAXCYC=0,NTMIN=1,
> NSTLIM=100000,DT=0.0001,NRESPA=1,
> NTT=3,TEMPI=0.0,TEMP0=10.0,VLIMIT=-1.0,GAMMA_LN=5.0,IG=-1,
> NTP=0,PRES0=1.0,TAUP=1.0,
> NTC=1,
> NTF=1,NTB=1,CUT=8.0,IFQNT=0,IGB=0,
> /
>
> And the .rst7 written is something like:
>
> default_name
> 143939 0.1000000E+02
> ************************************************************************
> ************************************************************************
> ************************************************************************
> ************************************************************************
> ************************************************************************
> ************************************7943.2606719************************
> ************************************************************************
> ************************************8664.4607917************************
>
> The .out file doesn't show any error so it seems the equilibration is being performed but the .rst7 output file is not.
> Thanks in advance
>
> Facu
>
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Received on Wed Jun 23 2021 - 06:30:03 PDT
