AW: Running NAMD via GROMACS topology

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Mon Aug 11 2014 - 00:33:15 CDT

 

Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag von Mike Makowski
Gesendet: Montag, 11. August 2014 01:05
An: namd-l_at_ks.uiuc.edu
Betreff: Re: namd-l: Running NAMD via GROMACS topology

 

‚ÄčI suppose I should provide a bit more information:

 

The last line of output prior to meeting any errors is:

 

USING GEOMETRIC MEAN TO COMBINE L-J SIGMA PARAMETERS

 

(note that it said arithmetic mean b‚Äčefore invoking vdwGeometricSigma).

 

Following this there are a series of lines with "ERROR" before proceeding and attempting a single simulation step with energies outputting a maximum value.

 

Well, what does these ERRORs contain ??

Did you minimize the system? What you observer most likely is just a bad starting structure having to high potential energy (superimposed atoms).

 

I hope this is clear.

Michael Makowski

University of California, Irvine

Department of Chemistry,

Chemical and Material Physics,

Irvine, CA 92617

Cell: 267 588 9865

Office: 949 824 5776

 

 

 

On Sun, Aug 10, 2014 at 3:44 PM, Mike Makowski <mmakowsk_at_uci.edu> wrote:

Hello NAMD community,

 

I'm attempting to run simulations using GROMACS topology and coordinate inputs. The coordinate input reads properly but I'm generating errors when reading in the Lennard-Jones parameters and the simulation crashes with atoms moving at very high velocities. Considering that GROMACS generally performs the geometric mean (unlike NAMD's arithmetic mean) to calculate molecular parameters, I tried applying the vdwGeometricSigma but it's not making a difference. I was also concerned that the units were incompatible so I modified the input for values in terms of angstroms but that also didn't seem to make a difference. Might there be anyone who knows how NAMD reads in GROMACS inputs and may provide more information than can be found on the NAMD website? Thanks in advance!

 

Best Regards,

Mike

 

Michael Makowski

University of California, Irvine

Department of Chemistry,

Chemical and Material Physics,

Irvine, CA 92617

Cell: 267 588 <tel:267%20588%209865> 9865

Office: 949 <tel:949%20824%205776> 824 5776

 

 

 

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