Thanks for your reply! I have a try, when I set up, ntx=1 irest=5,, dt=0.002,
ntf=2, ntc=2. The MD was stopped immediately: IREST ( 5) must be 0 or 1. NTX / IREST inconsistency *** input error(s). Then I checked the email-list, Prof. David, ever suggested someone use ntx=1 irest=0. When I try this, it worked well! This means it will not use the fomer velocity. Is it ok?
Rilei Yu
--- 10年4月9日，周五, Jason Swails <jason.swails.gmail.com> 写道：
发件人: Jason Swails <jason.swails.gmail.com>
主题: Re: [AMBER] vlimit exceeded for step
收件人: "AMBER Mailing List" <amber.ambermd.org>
日期: 2010年4月9日,周五,下午8:36
Exceeded vlimits are generally indicative of overlapping atoms. Try
printing to your trajectory every step for a small number of steps
(ntwx=1) and visualizing the result to see if you can tell which atoms
may be causing the problems.
You may try minimizing and carefully heating the system in order to
relieve those bad contacts. However, it appears as though you've
already run a short amount of MD and this run is a restart, so you
should probably set the variables "irest=1, ntx=5". Also, if you want
to run with a 0.002 timestep, you should be SHAKEing bonds involving
hydrogen atoms (as their frequencies are too high to use such a long
timestep). Do this with "ntf=2, ntc=2". Details can be found in the
manual.
Good luck!
Jason
On Fri, Apr 9, 2010 at 2:52 AM, Rilei Yu <yulaomao1983.yahoo.com.cn> wrote:
>
> Dear amber users,
>
> When I set up dt=0.001, everything goes well. However, when I try dt=0.002, some bugs appeared! I even found someone even asked such question in the mail-list, but I still found it could not solve my problem. Can anyone give me some help?
>
> Thanks in advance!
> Errors:
>
> NSTEP = 0 TIME(PS) = 520.000 TEMP(K) = 301.82 PRESS = 0.0
> Etot = -2855.6283 EKtot = 8299.2936 EPtot = -11154.9219
> BOND = 4225.1312 ANGLE = 3334.7581 DIHED = 4614.4087
> 1-4 NB = 1561.4318 1-4 EEL = 17477.0703 VDWAALS = -2055.3714
> EELEC = -40323.2236 EHBOND = 0.0000 RESTRAINT = 10.8731
> EAMBER (non-restraint) = -11165.7950
> ------------------------------------------------------------------------------
>
> vlimit exceeded for step 2; vmax = 20.7518
> vlimit exceeded for step 3; vmax = 53.0707
> vlimit exceeded for step 4; vmax = 91.7254
> vlimit exceeded for step 5; vmax = 85.5594
> vlimit exceeded for step 6; vmax = 84.2917
> vlimit exceeded for step 7; vmax = 86.0951
> vlimit exceeded for step 8; vmax = 81.3904
> vlimit exceeded for step 9; vmax = 81.6573
>
> Input:
>
> &cntrl
> ntx=1,
> irest=0,
> imin=0,
> ntpr=10,
> ntwx=10,
> ntwr=50,
> nstlim=5000,
> dt=0.002,
> ntt=3,
> gamma_ln = 1.0,
> temp0=300,
> tempi=300,
> tautp=1,
> igb=0,
> ntb=0,
> cut=15,
> ntr=1,
> fcap=10.0,
> ivcap=0,
> tol=0.000001,
> ntr=1, restraint_wt=10.0, restraintmask=':1-90, 93-140, 151-180, 196-234, 242-256, 265-278, 283-310, 322-360, 371-410',
> &end
>
> Rilei Yu
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Fri Apr 09 2010 - 17:00:04 PDT
