Hello,
I am trying to run a pulling simulation with gromacs 4.0.2.
I have appended the following pull code to the mdp file:
;---PULL CODE -
pull= umbrella
pull_geometry = direction
pull_group0 = r_500
pull_group1 = r_535
pull_vec1 = -1.306
Hi,
You don't indicate which xvg file was 0, I guess pullf.xvg.
Could it be that you did not specify a force constant, meaning fc=0?
Berk
From: gene...@gmail.com
To: gmx-users@gromacs.org
Date: Tue, 13 Jan 2009 14:26:47 +0300
Subject: [gmx-users] Pull Code problems
Hello,
I am trying
2009 14:26:47 +0300
Subject: [gmx-users] Pull Code problems
Hello,
I am trying to run a pulling simulation with gromacs 4.0.2.
I have appended the following pull code to the mdp file:
;---PULL CODE -
pull = umbrella
pull_geometry = direction
which xvg file was 0, I guess pullf.xvg.
Could it be that you did not specify a force constant, meaning fc=0?
Berk
From: gene...@gmail.com
To: gmx-users@gromacs.org
Date: Tue, 13 Jan 2009 14:26:47 +0300
Subject: [gmx-users] Pull Code problems
Hello,
I am trying
OK,
I have a new problem.
I`ve started the simulation with the following pull parameters
;---PULL CODE -
pull--=- umbrella
pull_geometry-= direction
pull_group0--= r_500
pull_group1---= r_535
pull_vec1-= -1.306 1.355 -0.319
pull_k1--= 1000
things
that were possible before (and more).
Berk
Subject: Re: [gmx-users] Pull Code problems
From: gene...@gmail.com
To: gmx-users@gromacs.org
Date: Tue, 13 Jan 2009 18:44:36 +0300
OK,
I have a new problem.
I`ve started the simulation with the following pull parameters
of the whole system.
The AFM option is no longer there.
I never understood what the difference between Umbrella and AFM was.
But Umbrella (as well as constraint) should be able to do all things
that were possible before (and more).
Berk
Subject: Re: [gmx-users] Pull Code problems
From: gene
Hi,
If you pull without a reference, you will be doing nothing in the limit
of slow pulling. For fast pulling you will be doing something.
pull_start=yes
pull_init1=0
will initialize set pull_init to the initial distance.
Berk
Subject: RE: [gmx-users] Pull Code problems
From: gene
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