Re: [AMBER] which part of source code implementing GB/SA simulations?

From: case <>
Date: Tue, 14 Aug 2012 22:30:49 -0400

On Tue, Aug 14, 2012, Xin Geng wrote:
> I want to read the source code for GB/SA simulations and
> find file egb.f. In the subroutine egb(x,f,...,...), I find the "if(gbsa ==
> 2) then " and "if (gbsa ==1) then" . I think they are use to control
> different models. Now what I want to do is to add another "if" sentence to
> use another model, e.g. "if (gbsa == 3) then call XXX"(XXX is the
> subroutine for my model). But when I change the code it seems nothing
> happens. For example, I add "esurf = 1.0d0" after "# include 'gbsa.h'",but
> when I run "minimization", the result shown in "mdinfo" is the same as
> before.(Actually, no matter what I add to change the value of esurf and
> totsasa after "# include 'gbsa.h'" , the value of "esurf" shown in "mdinfo"
> is the same.)

We need more details, starting with which version of Amber you are looking
at. When you say you added "esurf=1.0" after "#include gbsa.h", do you mean
immediately after? Whatever value you assign to esurf immediately after
the include line will be overwritten by the "esurf = surften*totsasa" shortly
after that.

Of course, for debugging purposes, you should print out esurf
right at that point in the code, to check that it is not being changed
somewhere else before being printed in the mdinfo file. Unless you are
willing and able to do such basic programming tasks, I doubt that people on
the list will be able to help much. See if you can get one of the many
experienced people in your group to look at your code and provide some
immediate feedback.

...good luck...dac

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Received on Tue Aug 14 2012 - 20:00:04 PDT
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