Re: Re: namd simulation​:protein,l​igand,lipi​d,water and ions

From: Marlet Martinez (marletm8_at_gmail.com)
Date: Thu Jun 21 2012 - 09:59:09 CDT

Dear namd users,

Thank you so much for your suggestions.

I set tcl forces "off" and now my simulation is running :-)

Best wishes,

Mar

2012/6/19 Aron Broom <broomsday_at_gmail.com>

> Have you been able to successfully run a simulation with a different
> system, such as one of the benchmarks on the NAMD site? I would first try
> that, with the provided configuration files. If that works, then I would
> use those coordinate and parameter files with your configuration. If that
> still works, then it is likely you have something incorrect in your
> coordinates/topology/parameters.
>
> ~Aron
>
> On Tue, Jun 19, 2012 at 1:33 PM, Marlet Martinez <marletm8_at_gmail.com>wrote:
>
>> Dear all,
>>
>> Thanks for your suggestions,
>>
>> I already installed the 2.8 namd version but I cant run my
>> simulation, it stops again after message below comes (I already attached
>> my .log file in the previous message). I am thinking maybe there is one
>> problem in my simulation because no matter what version I use (2.6 or
>> 2.8) my simulation stops automatically and coordinates are not even
>> generated form the 02.conf
>>
>>
>> -----------------------------
>>
>> Info: CREATING 1716 COMPUTE OBJECTS
>>
>> Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625
>>
>> Info: NONBONDED TABLE SIZE: 769 POINTS
>>
>> Info: INCONSISTENCY IN FAST TABLE ENERGY VS FORCE: 0.000325096 AT 11.9556
>>
>> Info: INCONSISTENCY IN SCOR TABLE ENERGY VS FORCE: 0.000324844 AT 11.9556
>>
>> Info: INCONSISTENCY IN VDWA TABLE ENERGY VS FORCE: 0.0040507 AT 0.251946
>>
>> Info: INCONSISTENCY IN VDWB TABLE ENERGY VS FORCE: 0.00150189 AT 0.251946
>>
>> ---------------
>>
>> I would appreciate any suggestion,
>>
>> Thanks in advance,
>>
>> Mar,
>>
>>
>>
>
>
>
> --
> Aron Broom M.Sc
> PhD Student
> Department of Chemistry
> University of Waterloo
>
>

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