From: Chris Harrison (charris5_at_gmail.com)
Date: Wed Feb 15 2012 - 15:29:59 CST
Dear Sudipta,
This appears to be a problem involving the fep analysis tool in VMD.
While I can't promise anything, you might have much better luck asking
over on the vmd-l list about this particular problem.
(www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/)
Best,
Chris
On Tue, Jan 31, 2012 at 11:41 AM, sudipta <sudipta.mml_at_gmail.com> wrote:
> Hi everyone,
>
> I want to perform FEP calculations using NAMD. Therefore, I have finished my
> calculation according to tutorial and want to estimate the error of free
> energy (BAR estimator) by using the parsefep plugin of VMD (v 1.9).
> However, during this analysis, I am getting an error constantly that I
> cannot resolve it. I put the error message below.
>
> Error: domain error: argument not in valid range.
>
> I have divided the whole path as
>
> runFEP 0.0 0.01 0.001 $numSteps
> runFEP 0.01 0.1 0.01 $numSteps
> runFEP 0.1 0.9 0.1 $numSteps
> runFEP 0.9 0.99 0.01 $numSteps
> runFEP 0.99 1.0 0.001 $numSteps
>
> for forward direction and
>
> runFEP 1.0 0.99 -0.001 $numSteps
> runFEP 0.99 0.9 -0.01 $numSteps
> runFEP 0.9 0.1 -0.1 $numSteps
> runFEP 0.1 0.01 -0.01 $numSteps
> runFEP 0.01 0.0 -0.001 $numSteps
>
> for backward direction
> I have chosen the numSteps as 1500 and alchequilsteps as 500
>
> Insted of this above division, if I choose those as
>
> runFEP 0.0 0.1 0.001 $numSteps
> runFEP 0.1 0.9 0.01 $numSteps
> runFEP 0.9 1.0 0.001 $numSteps
>
> runFEP 1.0 0.9 -0.001 $numSteps
> runFEP 0.9 0.1 -0.01 $numSteps
> runFEP 0.1 0.0 -0.001 $numSteps
>
> for forward and backward direction then the calculations are finished
> without any error. So, what is my wrong?
>
> Can anyone highlight in this regard.
>
> Thanks
> Sudipta
>
> --
> ==========================================================
> Dr. Sudipta Kumar Sinha ||
> Postdoctoral Employee ||
> C/O Prof. Leonor Saiz ||
> Department Of Biomedical Engineering ||
> University of California, Davis ||
> U.S.A ||
> Email-sudipta.mml_at_gmail.com ||
> ==========================================================
>
>
-- Chris Harrison, Ph.D. Theoretical and Computational Biophysics Group NIH Resource for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801 char_at_ks.uiuc.edu Voice: 773-570-6078 http://www.ks.uiuc.edu/~char Fax: 217-244-6078
This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:21:13 CST