Re: Fatal Error Periodic cell has become too small for original patch grid

From: bharat gupta (bharat.85.monu_at_gmail.com)
Date: Fri Jul 01 2011 - 00:59:56 CDT

Hi,

I am doing the npt simulation using the following parameters:-

dielectric 1.0
coordinates ../common/complex_ionized.pdb

outputEnergies 1000
binaryoutput no
DCDFreq 1000
restartFreq 1000
binCoordinates ./equilibrated.restart.coor
binVelocities ./equilibrated.restart.vel
binaryrestart yes
structure ../common/complex_ionized.psf
paraTypeCharmm on
parameters ../common/par_all27_prot_na.prm
exclude scaled1-4
1-4scaling 1.0
switching on
switchdist 8.0
cutoff 12.0
pairlistdist 13.5
margin 0.0
stepspercycle 20
extendedSystem ./equilibrated.xsc
outputname dyn1-out

LangevinPiston on
LangevinPistonPeriod 100.0
LangevinPistonDecay 50.0
LangevinPistonTarget 1.01325 # constant pressure
LangevinPistonTemp 300 # constant temperature

numsteps 50000000 # 10 ns MD

I am getting the following error:-
Fatal Error Periodic cell has become too small for original patch grid

Also checked that restart.coor file I found that the water box got distorted
together with some of the residues of the protein. What shall I do in this
case. Is it because that I didn't specify the PBC parameters or what shall I
do to rectify it ....

-- 
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46010_at_yahoo.com

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