AMBER Archive (2006)

Subject: AMBER: Error message in methane solvent system

From: Atsutoshi Okabe (okabe_at_cherry.bio.titech.ac.jp)
Date: Thu Dec 07 2006 - 21:19:04 CST

Dear all,

I executed sander program to equilibrate the system in methane solvent box.

But I got the following error message in output file.

＊＊＊＊＊＊＊＊＊＊＊＊＊＊＊＊＊＊＊＊＊＊＊＊＊＊＊＊＊＊＊＊＊＊＊＊＊＊

NSTEP = 32400 TIME(PS) = 78.800 TEMP(K) = 296.90 PRESS =
116.7

 Etot = 3409.4640 EKtot = 2349.6920 EPtot =
1059.7720

 BOND = 10.2431 ANGLE = 1222.7808 DIHED =
51.9193

 1-4 NB = 10.1691 1-4 EEL = 140.2031 VDWAALS =
-256.9207

 EELEC = -137.2042 EHBOND = 0.0000 RESTRAINT =
18.5814

 EAMBER (non-restraint) = 1041.1905

 EKCMT = 628.4852 VIRIAL = 149.0902 VOLUME =
190305.2399

                                                    Density =
0.1032

 Ewald error estimate: 0.1011E-01

---------------------------------------------------------------------------- 

--

 SANDER BOMB in subroutine nonbond_list

  volume of ucell too big, too many subcells

  list grid memory needs to be reallocated, restart sander

I ran constant pressure and set temperature 298K

#equilibration(500ps)

 &cntrl

 ntpr=200,ntwx=1000,ntave=1000,

 ntb=2, ntp=1,

 ntf=2,  ntc=2,

 ntt=1,  tautp=0.5, temp0=298.0,

 taup=1.0,

 iwrap=1,

 dt=0.002,  nstlim=250000,

 ntr=1,

 restraint_wt=100.0,

 restraintmask=':1-2',

 /

I can’t understand why I got the error message.

Could you please give me any suggestions to solve this problem?

Thanks,

Atsutoshi

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu