[AMBER] Amber:SANDER BOMB:volume of ucell too big, too many subcells

From: shradhey gupta <shradhey.iitk.ac.in>
Date: Wed, 21 Dec 2011 11:40:17 +0530

dear all,

i am facing problem to run md simulation of pure methanol of 367 molecules
in 42875A box after minimization. at the end of md simulation, file has
terminated with error line as,
----------------------------------------------------------------------------

 NSTEP = 87250 TIME(PS) = 107.250 TEMP(K) = 292.11 PRESS =
173.6 Etot = 2843.7295 EKtot = 2588.3536 EPtot =
255.3759 BOND = 177.4774 ANGLE = 1165.5481 DIHED =
 211.4788 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS =
-1299.1285 EELEC = 0.0000 EHBOND = 0.0000 RESTRAINT =
     0.0000 EKCMT = 577.2348 VIRIAL = 333.6967 VOLUME =
  64978.1091
                                                Density = 0.5216
----------------------------------------------------------------------------

"SANDER BOMB in subroutine nonbond_list
volume of ucell too big, too many subcells
list grid memory needs to be reallocated, restart sander"

i did not get actual problem, is this problem in md input file or system
input file. when it run the md simulation, i observed that volume of box
is becoming bigger and bigger with simulation run time as well as decrease
in density. the details of md input file is as

 imin = 0,
  irest = 1,
  ntx = 7,
  ntb = 2,
  iwrap = 1,
  pres0 = 1.0,
  ntp = 1,
  taup = 2.0,
  cut = 10.0,
  ntr = 0,
  ntc = 2,
  ntf = 2,
  ips = 1,
  tempi = 300.0,
  temp0 = 300.0,
  ntt = 3,
  gamma_ln = 1.0,
  nstlim = 200000, dt = 0.001,
  ntpr = 250, ntwx = 250, ntwr = 10000
 /

can you tell me what is wrong and why? if you good-self have any
suggestion to make this problem fix, please let me know.

thanks in advance.

Shradhey Gupta


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Received on Tue Dec 20 2011 - 22:30:02 PST
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