Thanks for your reply. This thim , I did the heating in serial mode, and there is a error message (vlimit exceeded for step 0; vmax = 20.1728). Moreover, the potential energy at the beginning of MD (-15181) doesn't matches that at the end of minimization (-13176),but for the examples of amber tutorial (
http://ambermd.org/tutorials/basic/tutorial1/section5.htm), the potential energy at beginning of MD (-44677) doesn't match that at the end of minimization (-41777) though.
This is the output file,
| Local SIZE OF NONBOND LIST = 772152
| TOTAL SIZE OF NONBOND LIST = 772152
NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS = 0.0
Etot = -15181.2108 EKtot = 0.0000 EPtot = -15181.2108
BOND = 2.2808 ANGLE = 61.4491 DIHED = 6.7048
1-4 NB = 4.7038 1-4 EEL = -193.6156 VDWAALS = 3412.7372
EELEC = -18475.4708 EHBOND = 0.0000 RESTRAINT = 0.0000
Ewald error estimate: 0.2619E-04
------------------------------------------------------------------------------
vlimit exceeded for step 0; vmax = 20.1728
NSTEP = 1 TIME(PS) = 0.002 TEMP(K) = 654.81 PRESS = 0.0
Etot = -11269.0658 EKtot = 3912.1450 EPtot = -15181.2108
BOND = 2.2808 ANGLE = 61.4491 DIHED = 6.7048
1-4 NB = 4.7038 1-4 EEL = -193.6156 VDWAALS = 3412.7372
EELEC = -18475.4708 EHBOND = 0.0000 RESTRAINT = 0.0000
Ewald error estimate: 0.2619E-04
------------------------------------------------------------------------------
vlimit exceeded for step 1; vmax = 532.5056
NSTEP = 2 TIME(PS) = 0.004 TEMP(K) = NaN PRESS = 0.0
Etot = NaN EKtot = NaN EPtot = 24890.4910
BOND = 2.2645 ANGLE = 61.4926 DIHED = 6.7032
1-4 NB = 4.6909 1-4 EEL = -193.5540 VDWAALS = 3901.9997
EELEC = -13832.0968 EHBOND = 0.0000 RESTRAINT = 34938.9910
EAMBER (non-restraint) = -10048.5000
Ewald error estimate: 0.1777E-03
------------------------------------------------------------------------------
> -----原始邮件-----
> 发件人: "David A Case" <case.biomaps.rutgers.edu>
> 发送时间: 2014年11月11日 星期二
> 收件人: "AMBER Mailing List" <amber.ambermd.org>
> 抄送:
> 主题: Re: [AMBER] a problem on heating the system
>
> On Tue, Nov 11, 2014, ZHAO Ruisheng wrote:
>
> > Thanks very much for your reply. I have peformed the heating process
> > according your suggestions (ntpr=1), and the heating process proceeds a
> > few steps beforing stoping. I noticed that the system bursted from the
> > obtained restrart file. Dose this mean that the minimization prior to MD
> > was too short and I need to perform a longer minimization? This is the
> > output file,
>
> There is likely something different about the system you minimized
> and the one you are doing MD on. Make sure the the potential energy at the
> beginning of the MD run (-15181) matches that at the end of the minimization.
>
> It might be that all you need is more minimization, but your symptoms are
> those of a more fundamental problem, but we don't have enough information
> to say that that problem is.
>
> You didn't say if you ran the job in serial mode or not. Be sure to do that
> if you have not already done so.
>
> ....regards...dac
>
>
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Received on Tue Nov 11 2014 - 05:00:02 PST
