Dear Dr. Jason,
Now, the problem has been solved! Next time, I should be more cautious!
Thanks for your remind!
Rilei Yu
--- 10年4月10日，周六, 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10日,周六,上午7:59
On Fri, Apr 9, 2010 at 7:50 PM, Rilei Yu <yulaomao1983.yahoo.com.cn> wrote:
> Thanks for your reply! I have a try, when I set up, ntx=1 irest=5,, dt=0.002,
If you look more closely at the previous email, you will see that it
says "ntx=5, irest=1", you have it backwards. The manual also
explains this explicitly.
Good luck,
Jason
> 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
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
>
> _______________________________________________
> 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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Apr 10 2010 - 01:00:02 PDT
