Re:Re: [AMBER] the volume is always getting bigger and bigger until crash

From: Yunfen Wang <wangfen041237.163.com>
Date: Thu, 15 Apr 2010 08:47:38 +0800 (CST)

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 !



2010-04-14 18:05:14"Carlos Simmerling" <carlos.simmerling.gmail.com> д
>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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Received on Wed Apr 14 2010 - 18:00:03 PDT
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