From: amin_at_imtech.res.in
Date: Tue Sep 04 2012 - 02:12:37 CDT
Hi,
I agree that was a mistake by me. It happened because I measured water to set
the cell size as given in the tutorial. But the POPCs stick out of the water
box in the xy plane,which is also mentioned in the tutorial. In my particular
case the extra 1 A was not enough, so when I measured the x y dimensions of
the POPC layer and adjusted cell size accordingly, I got rid of "constraints"
error. But even after making the required changes in the cell size, the issue
of overlapping atoms doesn't go away and the VDW energies are still 99999999,
probably showing that the problem is more than the cell dimensions. So your
idea of adding such a warning in building stage would be very helpful.
Regards.
Amin.
> Hi,
>
> I think it would make sense to add such a warning at a system building
> stage, maybe for psfgen. Such a "simple" structure check is also implemented
> in the amber tools. For example, when doing saveamberparm in xleap, which is
> the same as psfgen for charmm, messages like "Close contact between x and y"
> or "There is an bond of 7A between x and y" or "The total charge of the
> system is not zero". At this stage of using VMD as a system building tool
> (and not as visualizer) it would be a nice thing IMHO.
>
> Nevertheless, if someone builds a system, set a box dimension, solvate it,
> then use different cell size in the simulation and wonders about
> superimposed atoms, even such a feature can't help. -_-
>
> Norman Geist.
>
>> -----Ursprüngliche Nachricht-----
>> Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
>> Auftrag von Axel Kohlmeyer
>> Gesendet: Montag, 3. September 2012 22:28
>> An: Rajan Vatassery
>> Cc: amin_at_imtech.res.in; Norman Geist; namd-l_at_ks.uiuc.edu
>> Betreff: Re: AW: AW: AW: namd-l: Error in membrane protein simulation
>>
>> Well then here is your chance to win the eternal gratitude of all VMD
>> or NAMD users that share your sentiment.
>> axel
>> ------Original Message------
>> From: Rajan Vatassery
>> To: Axel Kohlmeyer
>> Cc: amin_at_imtech.res.in
>> Cc: Norman Geist
>> Cc: namd-l_at_ks.uiuc.edu
>> ReplyTo: Rajan Vatassery
>> Subject: Re: AW: AW: AW: namd-l: Error in membrane protein simulation
>> Sent: Sep 3, 2012 10:15 PM
>>
>> looks like we agree that it would be easy to do.
>>
>> On Mon, 2012-09-03 at 22:13 +0200, Axel Kohlmeyer wrote:
>> > On Mon, Sep 3, 2012 at 10:03 PM, Rajan Vatassery <rajan_at_umn.edu>
>> wrote:
>> >
>> > > On a related note, I think VMD could add an error message
>> in cases
>> >
>> > VMD is a visualizer there doesn't care much what kind of data you
>> feed it.
>> >
>> > > where atoms are superimposed. While it wouldn't be widely useful,
>> it
>> > > would be easy enough to implement that it would be worthwhile
>> > > expenditure of time.
>> >
>> > you can easily write such a check with a few lines of VMD script
>> code.
>> > (loop over all atoms, create a selection with a reasonably short
>> cutoff
>> > around the current atom index, count the atoms in the selection, if
>> it
>> > more than 1 throw a warning, delete the selection).
>> >
>> > cheers,
>> > axel.
>> >
>> > > rajan
>> >
>>
>>
>>
>> --
>> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
>> International Centre for Theoretical Physics, Trieste. Italy.
>
>
>
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