[gmx-users] Pull Code problems

2009-01-13 Thread DimitryASuplatov
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

RE: [gmx-users] Pull Code problems

2009-01-13 Thread Berk Hess
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

RE: [gmx-users] Pull Code problems

2009-01-13 Thread DimitryASuplatov
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

RE: [gmx-users] Pull Code problems

2009-01-13 Thread Berk Hess
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

Re: [gmx-users] Pull Code problems

2009-01-13 Thread DimitryASuplatov
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

RE: [gmx-users] Pull Code problems

2009-01-13 Thread Berk Hess
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

RE: [gmx-users] Pull Code problems

2009-01-13 Thread DimitryASuplatov
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

RE: [gmx-users] Pull Code problems

2009-01-13 Thread Berk Hess
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