Re: implicit solvent job error in NAMD2.8b1

From: David Tanner (guacamoleo_at_gmail.com)
Date: Tue Apr 05 2011 - 11:35:49 CDT

Yes, you can use this implicit solvent with lipids. Because PME is not
compatible with GBIS, PBC are not required. Because they would only
add work, simulations would run faster without PBC. As to how PBC
might change your structure, I don't know.

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
David E. Tanner
Theoretical and Computational Biophysics Group
3159 Beckman Institute
University of Illinois at Urbana-Champaign
405 N. Mathews
Urbana, IL 61801
http://www.linkedin.com/in/davidetanner
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

On Apr 4, 2011, at 5:14 PM, harish vashisth wrote:

Dear David,
   Thanks for your prompt reply. It was certainly some issue with the
PDB file, but not related to minimization. Because same files worked
fine in an explicit solvent run, I had no reason to believe that there
is some issue with not so well minimized coordinates. The problem
turned out to be that when i extracted just the protein coordinates
from the originally solvated and ionized files of this protein to
launch an implicit solvent run, some water molecules also sneaked in
due to not stringent enough atom selection that I made. Run is going
fine now, but after 500 steps of minimization, it shows the kind of
output below. I think it is normal which is simply reporting writing
dcd files every 10 frames. I have another question. Can we use the
same implicit solvent model in an explicit protein-membrane system
with lets say POPC/POPE type of lipids? Secondly question is what
difference does it make if we use PBC or not use them as the User's
guide suggests them optional? Thanks again for all the help!

=======================================================
WRITING COORDINATES TO DCD FILE AT STEP 500
The last position output (seq=500) takes 0.000 seconds, 25.560 MB of
memory in use
REINITIALIZING VELOCITIES AT STEP 500 TO 310 KELVIN.
TCL: Running for 1000000 steps
WRITING COORDINATES TO DCD FILE AT STEP 510
The last position output (seq=510) takes 0.000 seconds, 25.600 MB of
memory in use
WRITING COORDINATES TO DCD FILE AT STEP 520
The last position output (seq=520) takes 0.000 seconds, 25.913 MB of
memory in use
WRITING COORDINATES TO DCD FILE AT STEP 530
The last position output (seq=530) takes 0.000 seconds, 25.925 MB of
memory in use
WRITING COORDINATES TO DCD FILE AT STEP 540
The last position output (seq=540) takes 0.000 seconds, 25.826 MB of
memory in use
WRITING COORDINATES TO DCD FILE AT STEP 550
The last position output (seq=550) takes 0.000 seconds, 25.873 MB of
memory in use
WRITING COORDINATES TO DCD FILE AT STEP 560
The last position output (seq=560) takes 0.000 seconds, 26.151 MB of
memory in use
WRITING COORDINATES TO DCD FILE AT STEP 570
The last position output (seq=570) takes 0.000 seconds, 26.030 MB of
memory in use
WRITING COORDINATES TO DCD FILE AT STEP 580
The last position output (seq=580) takes 0.000 seconds, 26.203 MB of
memory in use
WRITING COORDINATES TO DCD FILE AT STEP 590
The last position output (seq=590) takes 0.000 seconds, 26.114 MB of
memory in use
=====================================================================

On Mon, Apr 4, 2011 at 5:34 PM, David Tanner <guacamoleo_at_gmail.com>
wrote:
The below output is normal for systems with atoms which are initially
very close together such that their repulsive forces are very large.
Try minimizing this same system in vacuum (no explicit water and GBIS
turned off) to verify that your problem is not with implicit solvent
but rather a problem with the system's initial coordinates.

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
David E. Tanner
Theoretical and Computational Biophysics Group
3159 Beckman Institute
University of Illinois at Urbana-Champaign
405 N. Mathews
Urbana, IL 61801
http://www.linkedin.com/in/davidetanner
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

On Apr 4, 2011, at 3:47 PM, harish vashisth wrote:

Dear all,
    I am sorry if anyone is getting this email twice. I have been
trying to use new implicit solvent feature in recently released
NAMDv2.8b1 (64 bit Linux_X86_64 binary and ran using ++local option).
I tried default options suggested in NAMD user's guide (http://www.ks.uiuc.edu/Research/namd/2.8b1/ug/node31.html
), and have tried both with and without PBCs, but I start getting some
weird output right at the beginning of these runs. No dcd files are
updated after two or three frames. The kind of output I get during
initial minimization steps looks like as given below.
The input files for this run can be downloaded from the following link:

        http://sitemaker.umich.edu/harish.vashisth/home

  Any help would be great. Thank you so much.

==============================
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========================================================================
MINIMIZER SLOWLY MOVING 1 ATOMS WITH BAD CONTACTS DOWNHILL
PRESSURE: 27 2198.64 98.2676 21.3003 98.2676 2114.29 -160.482 21.3003
-160.482 2326.12
GPRESSURE: 27 nan nan nan nan nan nan nan nan nan
ENERGY: 27 142506.0681 34522.7769 1025.3743
51.7267 -958225.7788 9999999999.9999 0.0000
0.0000 0.0000 9999999999.9999 0.0000
9999999999.9999 9999999999.9999 0.0000 2213.0139
9999999999.9999 555899.7610 2213.0139 9999999999.9999

MINIMIZER SLOWLY MOVING 1 ATOMS WITH BAD CONTACTS DOWNHILL
PRESSURE: 28 2198.99 97.9171 21.2457 97.9171 2116.46 -161.112 21.2457
-161.112 2326.4
GPRESSURE: 28 nan nan nan nan nan nan nan nan nan
ENERGY: 28 142507.7791 34521.3553 1024.9075
50.3971 -958456.7341 9999999999.9999 0.0000
0.0000 0.0000 9999999999.9999 0.0000
9999999999.9999 9999999999.9999 0.0000 2213.9492
9999999999.9999 555899.7610 2213.9492 9999999999.9999

MINIMIZER STARTING CONJUGATE GRADIENT ALGORITHM
LINE MINIMIZER REDUCING GRADIENT FROM nan TO nan
LINE MINIMIZER BRACKET: DX 0 0 DU 0 0 DUDX nan nan nan
MINIMIZER RESTARTING CONJUGATE GRADIENT ALGORITHM
LINE MINIMIZER REDUCING GRADIENT FROM nan TO nan
LINE MINIMIZER BRACKET: DX 0 0 DU 0 0 DUDX nan nan nan
MINIMIZER RESTARTING CONJUGATE GRADIENT ALGORITHM
LINE MINIMIZER REDUCING GRADIENT FROM nan TO nan
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========================================================================

Regards,
-Harish Vashisth

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