AMBER Archive (2005)

Subject: AMBER: Problem during production!!

From: jpragati_at_ibab.ac.in
Date: Tue Oct 04 2005 - 03:33:48 CDT

Dear
I am facing problem while running Production.
Ihe AMBER Version is 7.
The machine i am using is PC and working on LINUX Platform.

Prevously when i am running SANDER at 405.200 PS i am getting some abrupt
values so i change the cut off from 9.0 to 10.0. The simulation is
running properly at 405.000 PS. The values are as follows:
**********************************************************
At 405.00 PS
NSTEP =182500 TIME(PS) = 405.000 TEMP(K) =298.60 PRESS =
19.58
Etot = -41007.9797 EKtot = 8606.5562 EPtot =
-49614.5359
BOND = 259.4087 ANGLE = 517.0682 DIHED =
619.7258
1-4 NB = 297.6053 1-4 EEL = -3762.4513 VDWAALS =
5697.8559
EELEC = -53243.7486 EHBOND = 0.0000 CONSTRAINT =
0.0000
EKCMT = 3895.3593 VIRIAL = 3835.3170 VOLUME =
142022.3680
                                                Density =
1.0341
 Ewald error estimate: 0.2726E-03

------------------------------------------------------------------------------
At 405.200 PS
vlimit exceeded for step 182599; vmax = 4.11788775E+305

NSTEP =182600 TIME(PS) = 405.200 TEMP(K) = nan PRESS
=**********
Etot = nan EKtot = nan EPtot =
-49510.1718
BOND = 246.8402 ANGLE = 478.0948 DIHED =
624.7833
1-4 NB = 286.4919 1-4 EEL = -3711.3995 VDWAALS =
5691.2558
EELEC = -53126.2384 EHBOND = 0.0000 CONSTRAINT =
0.0000
EKCMT = 3906.4178 VIRIAL = ************ VOLUME =
142128.5621
                                                Density =
1.0334
 Ewald error estimate: 0.6438E-04

-----------------------------------------------------------------------------
***********************************************************************************
By changing cut off the simulation is running properly at 559.800. But
after it the simulation stop suddenly by givimg such values:

OLD LIST LOGIC; ntnb = 1
 EWALD BOMB in subroutine setup_grids
 Resulting cutoff is too small for your lower limit
******************************************************************************

 NSTEP = 9900 TIME(PS) = 559.800 TEMP(K) = 297.54 PRESS = 120.27
 Etot = -41046.5754 EKtot = 8576.1318 EPtot = -49622.7071
 BOND = 255.3091 ANGLE = 536.4557 DIHED = 638.1792
 1-4 NB = 292.7408 1-4 EEL = -3781.9416 VDWAALS = 5630.6484
 EELEC = -53194.0986 EHBOND = 0.0000 CONSTRAINT = 0.0000
 EKCMT = 3913.4751 VIRIAL = 3544.9360 VOLUME = 141921.1952
                                                Density = 1.0349
 Ewald error estimate: 0.5295E-04
 ------------------------------------------------------------------------------

 OLD LIST LOGIC; ntnb = 1
 OLD LIST LOGIC; ntnb = 1
 OLD LIST LOGIC; ntnb = 1
 OLD LIST LOGIC; ntnb = 1
 OLD LIST LOGIC; ntnb = 1
 OLD LIST LOGIC; ntnb = 1
 OLD LIST LOGIC; ntnb = 1
 OLD LIST LOGIC; ntnb = 1
 OLD LIST LOGIC; ntnb = 1
 OLD LIST LOGIC; ntnb = 1
check COM velocity, temp: 0.000000 0.00(Removed)

Can you suggest what the problem is and how can i rectify it...
This step i had done repeatedly and encounter the same problem at this
step only.
It can be a kind help from your side.

Regards
Pragati 

-- 
Be ready when opportunity comes...Luck is the time when preparation and
opportunity meet.

                      *******
Pragati Jain
PGD-2004-'05
Institute of Bioinformatics and Applied Biotechnology
G-05, Tech Park Mall, International Technology Park
Whitefield Road, Bangalore 560 066, India
Tel: +91 (80) 2841-0029, 2841-2769
Fax: +91 (80) 2841-2761

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