From: harish vashisth (harish.vashisth_at_gmail.com)
Date: Mon Apr 04 2011 - 17:14:20 CDT
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.
>
> ==============================
>
> ====================================================================================================================
> 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
>
> ===============================================================================================================================================
>
>
> Regards,
> -Harish Vashisth
>
>
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