Hi,
'vlimit' errors are usually indicative of improper prior
equilibration. You may need more minimization prior to your production
run. Also, a cutoff of 12 Angstroms is far too small to be considered
reliable for a GB simulation. You should really run with an
effectively infinite cutoff (9999.0 is usually adequate), otherwise
you are omitting a lot of important interactions from your system.
-Dan
On Sat, Apr 16, 2016 at 10:43 AM, Avik Bhattacharjee <avik8394.gmail.com> wrote:
> Hi,
> I was trying to simulate a protein in implicit solvent environment. i have
> first minimized the structure and then tried to carry out a production MD
> in implicit solvent using the following input parameters:
>
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> *hca MD Generalised Born, 12 angstrom cut off &cntrl imin = 0, ntb = 0,
> igb = 1, ntpr = 500, ntwx = 500, ntt = 3, gamma_ln = 1.0, tempi = 300.0,
> temp0 = 300.0, nstlim = 100000, dt = 0.002, cut = 12.0 /*
>
> but as soon as I start the simulation the structure started to collapse.
> Here I am annexing a copy of the output file:
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> *vlimit exceeded for step 496; vmax = **********vlimit exceeded for
> step 497; vmax = **********vlimit exceeded for step 498; vmax =
> **********vlimit exceeded for step 499; vmax = ********** NSTEP =
> 500 TIME(PS) = 1.000 TEMP(K) =********* PRESS = 0.0 Etot
> = NaN EKtot = 19874662.4076 EPtot =
> NaN BOND = 852405.4613 ANGLE = 94829.9606 DIHED =
> 8798.7961 1-4 NB = 71329408.5341 1-4 EEL = 11302.8746 VDWAALS =
> ************** EELEC = -18466.3455 EGB = NaN
> RESTRAINT =
> 0.0000 ------------------------------------------------------------------------------vlimit
> exceeded for step 500; vmax = **********vlimit exceeded for step 501;
> vmax = **********vlimit exceeded for step 502; vmax = **********vlimit
> exceeded for step 503; vmax = **********vlimit exceeded for step 504;
> vmax = **********vlimit exceeded for step 505; vmax = **********vlimit
> exceeded for step 506; vmax = **********vlimit exceeded for step 507;
> vmax = **********vlimit exceeded for step 508; vmax = **********vlimit
> exceeded for step 509; vmax = ***********
> Please help me out
> *.*
>
> With regards,
> Avik Bhattacharjee
> IIT KGP
> INDIA*.*
> _______________________________________________
> AMBER mailing list
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> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Sat Apr 16 2016 - 10:00:07 PDT
