nobody will be able to help unless you give the details of your
solvent. we have no information about it so can't even guess.
On 4/14/10, Yunfen Wang <wangfen041237.163.com> wrote:
> Hello,
> My system is a protein consist of 129 amino acids .I solvate it with a
> new molecule. The new molecule is drawn myself . Is it the problem?
> The density is getting smaller and smaller , for the volume is getting
> bigger, from 0.2 originally to 0.02 later .
> Do you have some suggestions or explanation for this problem ?
> Thank you !
>
>
>
> 在2010-04-14 18:05:14，"Carlos Simmerling" <carlos.simmerling.gmail.com> 写道：
>>what is the system you are simulating? does it have any new parameters, or
>>is it all standard molecules?
>>what density does sander report?
>>
>>
>>2010/4/14 Yunfen Wang <wangfen041237.163.com>
>>
>>> Dear users,
>>> In my MD simulation, I found the volume is always getting bigger
>>> and
>>> bigger until crash. But the temperature is steady .
>>> The error reminding is that
>>> Error 1 : Sander bomb in subroutine nonbond_list
>>> volume of uncell too big ,too many subcells list grid
>>> memory needs to be reallocated ,restart sander
>>> when I meet it , I restart the input file and the running is continued
>>> But this time , I restart , it reminds the follow error and break the
>>> simulation
>>> Error 2 :
>>> At line 2441 of file -ew -setup.f (unit9 "***.rst")
>>> Traceback: not available , complile with
>>> - ftrace = frame or - ftrace = full
>>> Fortran runtime error :bad value duiring floating point
>>> read
>>> when Error 2 appeared , the simulation has crash
>>> This is my input file:
>>> &cntrl
>>> imin = 0, irest = 1, ntx = 7,
>>> ntb = 2, pres0 = 1.0, ntp = 1,
>>> taup = 0.5,
>>> iwrap = 1,
>>> cut = 10, ntr = 0,
>>> ntc = 2, ntf = 2,
>>> tempi = 300.0, temp0 = 300.0,
>>> tautp = 0.10000,ntt = 1,
>>> nstlim = 2000000, dt = 0.0005,
>>> ntpr = 500, ntwx = 500, ntwr = 500
>>> /
>>> What's the problem ? How can I continue my simulation ? Can anyone give
>>> me
>>> instructions ,Thank u in advance!
>>> sincerly ,
>>> wang
>>> _______________________________________________
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>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
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--
===================================================================
Carlos L. Simmerling, Ph.D.
Professor, Department of Chemistry
CMM Bldg, Room G80 Phone: (631) 632-1336 Fax: 632-1555
Stony Brook University E-mail: carlos.simmerling.gmail.com
Stony Brook, NY 11794-5115 Web: http://www.simmerlinglab.org
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Received on Wed Apr 14 2010 - 18:00:03 PDT
