Simulation in vaccum

From: bo baker (bo.bybaker_at_gmail.com)
Date: Fri Jan 06 2006 - 19:17:03 CST

Hello, NAMD:

I built two models of a transmembrane protein based on two different
templates. I would like to do some initial structure refinments:
subject the two models to minimization and short simulation in vacuum.
This would allow me to compare the two models in energy level as well
as geometry level. After this, the model will be inserted into
membrane and water for
futher MD simulation.

I am not sure if NAMD is good for this purpose, simulation protein
structure in vacuum. I couldn't find the tutorial or examples. I have
 tried some steps, but the run was stopped prematured.

Here is how I did:

--- minimization for 2000 steps
--- equil at 310 K for 25000 steps

Here are the error messages:
For model 1:

WRITING COORDINATES TO DCD FILE AT STEP 24000
TIMING: 24100 CPU: 2850.66, 0.1199/step Wall: 3000.94,
0.163925/step, 0.132051 hours remaining, 0 kB of memory in use.
ENERGY: 24100 543.6413 1486.1952 923.4096 =20
80.5016 -2664.1032 -311.3172 0.0000 =20
 0.0000 1922.0600 1980.3873 315.5194 =20
2010.7229 2002.7730 311.0336

FATAL ERROR: Periodic cell has become too small for original patch grid!
Possible solutions are to restart from a recent checkpoint,
increase margin, or disable useFlexibleCell for liquid simulation.

For model 2:

TIMING: 3200 CPU: 533.74, 0.1147/step Wall: 571.251, 0.121714/step,
0.804667 hours remaining, 0 kB of memory in use.
ENERGY: 3200 566.7572 1603.5447 1048.2289 =20
107.6930 -2211.1402 -255.1635 0.0000 =20
0.0000 2051.3032 2911.2233 312.3809 =20
2941.2697 2943.5047 311.9550

FATAL ERROR: Periodic cell has become too small for original patch grid!
Possible solutions are to restart from a recent checkpoint,
increase margin, or disable useFlexibleCell for liquid simulation.

I compare the TOTAL and rmsd of the two run. TOTAL are arond 1980
(model 1) and 2840 (model 2), rmsd are around 2.31 (model 1) and
2.341 (model 2). When I exam the trajectories, both structures move
around entirely but no big change in conformation.

 Thank you for advice!

Regards

Bo

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