Re: splitting up long run leads to very different DNA conformation in E field

From: JC Gumbart (
Date: Thu Jul 13 2006 - 20:55:43 CDT

Is this problem reproducible to the same degree of difference? Could
you give examples of your configuration files (the long run and, say,
one of the restart runs)?

Also, have you plotted the length over the course of the
simulations? It would be helpful to determine the time course of the
difference in length.

On Jul 13, 2006, at 6:40 PM, Todd Trimble wrote:

> Hi All,
> I am trying to look at the effect of an applied electric field on
> ssDNA
> conformation (one end fixed). The solvent is treated explicitly,
> along
> with counterions that neutralize DNA charge (128 Na + 99 Cl ions).
> The
> ionic strength is high, as is the E field strength (10mV/ang). I'm
> using the PME algorithm to handle the electrostatics. The problem I'm
> seeing is that I get very different results (i.e. end-to-end distance)
> when the simulation is carried out in a single run compared to when I
> split it into several shorter runs. The end-to-end distances in the 2
> cases are different by about 50%. The shorter simulations use the
> restart files (.coor, .vel, .xsc) of the previous simulation. The
> temperature and pressure setpoints are 300K and 1atm. The system has
> been through an extensive equilibration procedure prior to turning on
> the field. The volume of the cell does not seem to change much during
> simulation, and the PME grid size is around 1 ang. or less. I am also
> using 2 fs/step with all H bonds set to rigid.
> The initial electrostatic energy is identical to the final
> electrostatic
> energy from the previous simulation, but the initial potential
> energy is
> a little different than the final value of the previous simulation. I
> assumed that this was due to the regeneration of the PME grid at the
> start. Because the volume changes so little it's hard to believe that
> the generation of a new grid periodically could alter my results so
> drastically, but I can't think of anything else that is changing
> when I
> restart a simulation.
> Has anyone else had similar problems? Any advice would be greatly
> appreciated.
> Todd
> **********************************************************************
> Dr. Todd M. Trimble
> Asst. Professor of Research
> Center for Applied Nanobioscience at the Biodesign Institute
> Arizona State University
> work: 480-727-0435
> fax: 480-727-8283
> **********************************************************************

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