AMBER Archive (2003)

Subject: can you give me more advice about: vlimit exceeded when sander calculate free energies using TI

From: sxzheng (sxzheng_at_mail.shcnc.ac.cn)
Date: Mon Jun 16 2003 - 07:47:53 CDT

Dear amber,
I have test the system:
first, just take the ligand in waterbox it can run normally even with TI method
second, do the complex's dynamics in capwater condition with ibelly=0, it can run normally also with TI method
third, do the complex's dynamics in capwater condition with ibelly=1, it can run normally with no Ti method, but vlimit exceeded with TI method from the first step in clambda=0.0.

the error message:

| Local SIZE OF NONBOND LIST = 21035273
| TOTAL SIZE OF NONBOND LIST = 42040533
 vlimit exceeded for step 0 ; vmax = 15285.815760953277

 NSTEP = 1 TIME(PS) = 2.002 TEMP(K) = 4606.17 PRESS = 0.0
 Etot = 1147690.7491 EKtot = 57272.4173 EPtot = 1090418.3318
 BOND = 406.5912 ANGLE = 1251.2219 DIHED = 2354.7165
 1-4 NB = 882.5706 1-4 EEL = 10398.6365 VDWAALS = 1103229.4149
 EELEC = -28104.8198 EHBOND = 0.0000 RESTRAINT = 0.0000
 DV/DL = 6625.1759
 ------------------------------------------------------------------------------

 vlimit exceeded for step 1 ; vmax = 11285380.920467719

     Coordinate resetting (SHAKE) cannot be accomplished,
     deviation is too large
     NITER, NIT, LL, I and J are : 0 1 1032 5179 5178

     Note: This is usually a symptom of some deeper
     problem with the energetics of the system.

Thank you
sxzheng

ÔÚ 03-6-11 8:21:00 ÄúдµÀ£º
>On Wed, Jun 11, 2003, zsx wrote:
>
>> I have used the Cap water , ibelly=1 and ntb=0, it can run normally
>> dynamics in sander7, but when I use the normal dynamic *.rst as the input
>> file for sander7 TI calculation, icfe=1 and clambda=0.04691, the VDW energy
>> and Temperature will increase uncontrolly, then break down. I want to know
>> the reason, for it seem that it will go normally with period condition
>> system.
>
>There is probably some problem with your prmtop setup. The first thing you
>should always do with problems like this is run a 10-20 step simulation
>with ntpr=1. That way, you can see the energies and their differences in
>detail. If the reported DV/DL number is big, there is something wrong with
>the perturbed prmtop file. Try running short simulations at both lambda=0
>and lambda=1, and see if you can identify what the problems are.
>
>...good luck...dac
>
>--
>
>==================================================================
>David A. Case | e-mail: case_at_scripps.edu
>Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
>The Scripps Research Institute | phone: +1-858-784-9768
>10550 N. Torrey Pines Rd. | home page:
>La Jolla CA 92037 USA | http://www.scripps.edu/case
>==================================================================

                    ÖÂ
Àñ£¡

            sxzheng
            sxzheng_at_mail.shcnc.ac.cn