[gmx-users] Re: energy perturbation

[Farzad Molani]

Hi Mark
I read the manual and I used umabrella sampling and I got a curve for pmf but now I want to calculate pmf by energy perturbation that I want to sure about my curve that I got by umbrella sampling.
my question is about .itp file and how do I create.
thank you very much.

gmx-users-bounces at gromacs.org wrote: The results of your email command are provided below. Attached is your
original message.

- Results:
    Ignoring non-text/plain MIME parts

- Unprocessed:
    I read the manual and I used umabrella sampling and I got a curve for pmf=
     but now I want pmf by energy perturbation that I want to sure about my c=
    urve that I got by umbrella sampling.
    my question is about .itp file and how do I create.
    thank you very much.
    Mark Abraham  wrote: >
    > Hi Dear
    > I want to copute PMF between two amines by energy perturbation in
    > gromacs
    > but I do'nt know what do I?
    > I read the manual and mailing list but I cann't solve it. if you are
    > having
    > informatin please help me?
    You've been asking this question for months it seems, and you're not
    getting a substantive answer because it is too general. If you've read th=
    e
    manual, then you will have been able to choose one of several types of PM=
    F
    calculation implemented in GROMACS to do, and then to make further
    choices. Nobody is going to make these decisions for you. Maybe we'd
    provide advice if you laid out the pros and cons for the choices and we
    had suitable expertise.

- Ignored:
    
    For advice on asking questions the smart way so as to get useful answers,
    check out http://www.catb.org/~esr/faqs/smart-questions.html. In short,
    from that article, the more you're seen to be working toward your own
    solution, the more people are likely to want and be able to help you.
    
    Mark
    
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- Done.

Date: Tue, 8 Jan 2008 22:25:31 -0800 (PST)
From: Farzad Molani <farzad_c81 at yahoo.com>
Subject: Re: [gmx-users] energy perturbation
To: gmx-users-request at gromacs.org

 Hi Mark
I read the manual and I used umabrella sampling and I got a curve for pmf but now I want pmf by energy perturbation that I want to sure about my curve that I got by umbrella sampling.
my question is about .itp file and how do I create.
thank you very much.

Mark Abraham <mark.abraham at anu.edu.au> wrote: >
> Hi Dear
> I want to copute PMF between two amines by energy perturbation in
> gromacs
> but I do'nt know what do I?
> I read the manual and mailing list but I cann't solve it. if you are
> having
> informatin please help me?

You've been asking this question for months it seems, and you're not
getting a substantive answer because it is too general. If you've read the
manual, then you will have been able to choose one of several types of PMF
calculation  implemented in GROMACS to do, and then to make further
choices. Nobody is going to make these decisions for you. Maybe we'd
provide advice if you laid out the pros and cons for the choices and we
had suitable expertise.

For advice on asking questions the smart way so as to get useful answers,
check out http://www.catb.org/~esr/faqs/smart-questions.html. In short,
from that article, the more you're seen to be working toward your own
solution, the more people are likely to want and be able to help you.

Mark

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Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
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