AW: namd simulation:protein,ligand,lipid,water and ions

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Fri Jun 15 2012 - 01:20:45 CDT

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Hi,

it’s pretty strange that namd quits without any message. Could you maybe
also attach the configuration file for the problem simulation. And as
namd2.6 is pretty old, you could also try a newer build. For testing, the
precompiled would be enough so you don’t have to compile it by yourself.

Mit freundlichen Grüßen

Norman Geist.

Von: Marlet Martinez [mailto:marletm8_at_gmail.com]
Gesendet: Donnerstag, 14. Juni 2012 18:14
An: Norman Geist
Betreff: Re: namd-l: namd simulation:protein,ligand,lipid,water and ions

Dear Dr. Geist,

Thanks a lot for your attention. I have tried to re-stat 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 and dynamics have run well, but not in this
case because my simulation crashes few seconds later.

Do you think i may need to chenge my NAMD version?

Thank you so much,

Marlet

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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