AMBER Archive (2005)

Subject: AMBER: problem with pressure equilibration

From: Cenk Andac (cenk_andac_at_yahoo.com)
Date: Thu Jan 27 2005 - 16:23:59 CST


Dear amber folks

I have a solvated system which has been temperature
equilibrated at constant volume at 298.15 K. Now, I
would like to equilibrate pressure for my solvated
system.

Here is my input file:

 &cntrl
imin=0, nstlim=200,
dt=0.002, cut=5, irest=1, ntx=7,
ntt=3, gamma_ln= 30, tempi=298.15, temp0=298.15,
ntb=2, ntp=1, pres0=1, taup=1,
ntpr=10, ntr=1, cut=5,
 &end
Group input for restrained neamine
100.0
RES 1
END
END

after running sander, I get the following error
message at step 80

  

 NSTEP = 80 TIME(PS) = 20.160
TEMP(K) = 33578.05 PRESS = 59499.4
 Etot = 308060.0092 EKtot = 84675.3337
EPtot = 223384.6755
 BOND = 222354.5092 ANGLE = 21.0399
DIHED = 21.5635
 1-4 NB = 6.7852 1-4 EEL = 76.8398
VDWAALS = 1105.1769
 EELEC = -228.1304 EHBOND = 0.0000
RESTRAINT = 26.8914
 EAMBER (non-restraint) = 223357.7841
 EKCMT = 15435.9092 VIRIAL = -7414.3459
VOLUME = 17786.9092
                                                    
Density = 0.4762
 Ewald error estimate: 0.4939E+00
 -----------------------------------------

 vlimit exceeded for step 80 ;
vmax = 79.4825187420846
 SANDER BOMB in subroutine nonbond_list
  volume of ucell too big, too many subcells
  list grid memory needs to be reallocated,
   restart sander

Could someone please let me know how to solve the
problem above?

regards,

jenk.

                
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