Re: Error in Minimization

From: Axel Kohlmeyer (
Date: Sun Nov 08 2009 - 11:05:47 CST

On Sun, Nov 8, 2009 at 10:15 AM, Ale Gomez <> wrote:
> Hi Josh...
> Thanks for your answer. I want to study the behavior of bacteriorhodopsin in
> a lipid membrane. First I prepared my system: put the protein in a solvate,
> then in the lipid membrane and then remove extra atoms. I think that my
> prepared system is ok (probably not, that's the reason I attached the tcl
> script that I made). With my complete system I want to minimize it, then
> warm it up to 300 degrees and then try to equilibrate the system.


i don't think that this will work that easily. you have to follow a
more complex
protocol, where you keep parts of your system frozen and let other parts relax,
alternate between those frozen regions and then slowly let everything go.
a lipid membrane is not as rigid as a protein and you don't want for example
your lipid tails being kicked around (and turned around). secondly you have
to join multiple segments (the lipids, the protein and the water) and there you
have to avoid overlaps, but by that you create small areas of vacuum and those
will "implode" and leading to unstable dynamics and unwanted disorder in your
system (which would require very long equilibration time to get rid of).

just running minimize and then heat up, only works for trivial cases.

> When I ran the NAMD minimize script seems to be ok, but when it is finish I
> look into the log file and the values never change. It seems like that:
> LINE MINIMIZER BRACKET: DX 0 2.60819e-27 DU 0 0 DUDX -4.50299e+14
> -4.50299e+14 -4.50299e+14
> PRESSURE: 75 6.36711e+07 -195549 -1.28311e+06 -195549 6.28248e+07 -488651
> -1.28311e+06 -488651 7.24169e+07
> GPRESSURE: 75 4.91079e+07 -228040 -1.75324e+06 -225861 4.83403e+07 -447628
> -1.74294e+06 -588612 5.69508e+07
> ENERGY: 75 118703.4864 13094.4375 5678.0420
> 2300.9903 456312.2570 9999999999.9999 0.0000
> 0.0000 0.0000 9999999999.9999 0.0000 9999999999.9999
> 9999999999.9999 0.0000 66304287.8116 51466333.5562
> 427418.4400 66304287.8116 51466333.5562

> It seems like nothing change and in my opinion must change, am I right???.
> Probably I am making something wrong but I spent a lot of time trying to fix
> it but nothing happend. What you think??

well, have you looked at the _values_ they are _huge_. you seem to have some
very close contacts and they may even overlap, so that the minimizer does not
know where to go. have you inspected your system visually? there have
to be atoms
that are very close or conformations that have a very high energy.

you probably have to rebuild your system with larger safety margins and/or
do stepwise relaxations as explained above.


> Regards
> -------------------------------------------------------------------
> Ale Gomez
> Biophysics and Molecular Modelling Group
> Physics Department
> Escuela Politecnica Nacional, Quito-Ecuador
> Ladron de Guevara E11-253.
> Phone: 593-95292408
> 2009/11/8 Joshua Adelman <>
>> Hi Ale,
>> It is unclear from your email what the problem is you are attempting to
>> describe. You need to provide more detail into what you saw and what you
>> expected to see that makes you think the result is incorrect.
>> Best wishes,
>> Josh
>> On Nov 7, 2009, at 11:45 AM, Ale Gomez wrote:
>> Hi everyone.
>> I try to minimize a protein, bacrhodopsin, in a lipid membrane. But
>> everything looks great until minimize is ready. When I saw the log file
>> seems that anything had change. Could anybody help me.
>> I attached preparation script for vmd (preparacion.tcl) and minimize
>> script for namd (bacmin.conf).
>> Regards
>> -------------------------------------------------------------------
>> Ale Gomez
>> Biophysics and Molecular Modelling Group
>> Physics Department
>> Escuela Politecnica Nacional, Quito-Ecuador
>> Ladron de Guevara E11-253.
>> Phone: 593-95292408
>> <preparacion.tcl><bacmin.conf>

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
College of Science and Technology
Temple University, Philadelphia PA, USA.

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