From: Marlet Martinez (marletm8_at_gmail.com)
Date: Thu Jun 14 2012 - 12:29:15 CDT
2012/6/14 Marlet Martinez <marletm8_at_gmail.com>
Thanks, for you answer, I have tried to re-stated my simulation but it did
not work anyway. I am using NAMD 2.6 version, I wonder if that would be
problem.
>
> Yes, as far I could see, the message regarding" Inconsistency" is normal
> because I have seen it before in other simulations and they have run well,
> but not in this case because my simulation crashes few seconds later after
> this message.
>
> Do you think i may need to chenge my NAMD version?
>
> Thank you so much,
>
> Mar,
>
>
> 2012/6/14 Norman Geist <norman.geist_at_uni-greifswald.de>
>
>> Hi Marlet,****
>>
>> ** **
>>
>> you are right there is no concrete reason mentioned by namd why it
>> stopped, but it could be due to this inconsisteny complained at the end of
>> the log file. ****
>>
>> I will just say what I would try. As you are using the COMmotion
>> parameter and this is a new release, this is the only idea I have why the
>> energies/forces got changed at simulation start so I would try to remove
>> this parameter and see if it works. If this message is normal, forget what
>> I said.****
>>
>> ** **
>>
>> Otherwise, have you tried to start the simulation again to make sure it
>> wasn’t happenstance or something? You could also try namd2.8 so we see if
>> it is a problem of the new 2.9 release.****
>>
>> ** **
>>
>> Let us know****
>>
>> ** **
>>
>> Norman Geist.****
>>
>> ** **
>>
>> *Von:* owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] *Im
>> Auftrag von *Marlet Martinez
>> *Gesendet:* Donnerstag, 14. Juni 2012 01:45
>> *An:* namd-l_at_ks.uiuc.edu
>> *Betreff:* namd-l: namd simulation:protein,ligand,lipid,water and ions***
>> *
>>
>> ** **
>>
>> Dear All****
>>
>> I work with membrane protein NAMD simulations. My system consists of my
>> protein, ligand, lipid membrane, water, and ions. I have minimized my
>> lipid membrane and complex protein-ligand separately in order to have a
>> more relaxed system, and finally I could run the first configuration file
>> without having errors., however when I try to run the configuration file 02
>> my simulation automatically crashes and it does not say anything about it
>> (I attach log file).****
>>
>> I wonder if I may need to run other simulations prior to the the second
>> configuration file. I do not know for example if I may need a simulation to
>> release my ligand and then run the second (02.conf) configuration file.*
>> ***
>>
>> ****
>>
>> I would appreciate any suggestion regarding this issue,****
>>
>> ****
>>
>> Thanks in advance,****
>>
>> ****
>>
>> Mar,****
>>
>
>
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