AMBER Archive (2003)

Subject: Shake problem in organic solvent

From: yuan bo (yuanbous_at_yahoo.com)
Date: Fri Jan 24 2003 - 06:03:48 CST

Dear Amber user
I am doing MD for an protein in dimethyl sulfoxide
solvent. Tatol atom number is 8687 and box size is
70.73 61.87 64.95. At first, I perform minimization.
After runing 20ps NPT equilibration with protein
fixed, I do 100ps NPT equilibration without any
constrain. error message is presented. There are my
input file and final part of output file as follows

min=0, ntb=2, ntp=1, cut=12.0, ntwx=100, ntwe=100,
nstlim=10000, ntc=2,ntf=2, irest=1, ntx=5, dt=0.001,
ntt=1, ntpr=100
&end

NSTEP = 6500 TIME(PS) = 20.200 TEMP(K) = 1602.74
 PRESS = 239.36 Etot = 48824.6417 EKtot =
38730.6393 EPtot = 10094.0024 BOND =
14742.7572 ANGLE = 12317.5395 DIHED =
1497.8884 1-4 NB = 819.6500 1-4 EEL = 11583.7751
VDWAALS =-8219.4360 EELEC = -22648.1718 EHBOND =
0.0000 CONSTRAINT =0.0000 EKCMT =3162.2434
VIRIAL=1797.4631 VOLUME=264079.1857
                           Density = 0.7956
Ewald error estimate: 0.7065E-04

  EWALD BOMB in subroutine ewald_list volume of ucell
too big!! a regular restart should fix things
  
   If I chang NTC from 2 to 3 and NTF from 2 to 3,
every thing is ok. But I only want to constrain the
bond length with hydrogen. How can I fix the problem?
Are there significant influence on results if using
NTC=3 instead of NTC=2? Could shake constrain bond
length only for organic solvent? Or the NTC=2 is not
suitable for organic solvent? Are there one better way
to simulate MD in organic solvent?
  any suggestion and any help is welcome
Thanks
yb

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