Re: RE: AMBER: problem with MD simulation

From: Ye Mei <ymei.itcc.nju.edu.cn>
Date: Sat, 5 Mar 2005 09:46:24 +0800

Dear Ross,

Thank you very much for your reply. Due to the network failure, I waited for two days to check my job.
I followed the tutorial of DNA and simulate ethanol this time. I first run gaussian and antechamber to
build the prepi info of ethanol, using resp charge model. And then I solvate the solute in TIP3PBOX with
thickness 10.0A. I tried to perform 2 steps minimizations, followed by 2 steps md simulations. The failure
is in the second step md simulation. All the files are all in attachment.
Would you please help to check them and find if there is anything wrong within? Thank you in advance.

        

======= 2005-03-02 00:51:40 =======

>
>Dear Ye,
>
>> I followed the tutorial of DNA simulation and perform the
>> minimation and md simulation of a acetic acid.
>> In the second md step, it stops with the followin error message:
>> NSTEP = 11400 TIME(PS) = 42.800 TEMP(K) =
>> 297.51 PRESS = -205.3
>> Etot = -5006.8792 EKtot = 1129.4954 EPtot
>> = -6136.3746
>> BOND = 0.7220 ANGLE = 2.2301 DIHED
>> = 7.3177
>> 1-4 NB = 0.2971 1-4 EEL = -103.9216 VDWAALS
>> = 905.0687
>> EELEC = -6948.0886 EHBOND = 0.0000 RESTRAINT
>> = 0.0000
>> EKCMT = 582.8635 VIRIAL = 669.5663 VOLUME
>> = 19555.3011
>> Density
>> = 0.9750
>> Ewald error estimate: 0.3798E-04
>>
>> --------------------------------------------------------------
>> ----------------
>>
>> vlimit exceeded for step 11426 ; vmax = 60309066.7197193
>
>One of your atoms has flown off at a massive speed, probably because it
>collided with another atom. It is a little hard to decipher what has
>happened from your output file but I suspect the fact that the volume is
>large may be a warning sign. Are you running periodic boundaries here? What
>have you solvated your acetic acid in?
>
>It seems strange that the calculation suddenly failed after 42ps but perhaps
>it had gone wrong earlier. Try setting ntpr=1 and ntwx=1 and then watch the
>mdcrd file over a few hundred steps and see if you can see anything wrong.
>
>Without more information, input files etc we cannot help much more I am
>afraid.
>
>All the best
>Ross
>
>/\
>\/
>|\oss Walker
>
>| Department of Molecular Biology TPC15 |
>| The Scripps Research Institute |
>| Tel:- +1 858 784 8889 | EMail:- ross.rosswalker.co.uk |
>| http://www.rosswalker.co.uk/ | PGP Key available on request |
>
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= = = = = = = = = = = = = = = = = = = =
                        

       
 
Best regards,
                                 
Ye Mei
ymei.itcc.nju.edu.cn
Institute of Theoretical and Computational Chemistry
School of Chemistry and Chemical Engineering
Nanjing University
Nanjing 210093
P.R.China
2005-03-04



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Received on Sat Mar 05 2005 - 02:53:00 PST
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