[gmx-users] REMD with umbrella sampling in Gromacs 4.5.5

2012-11-21 Thread Lin, Dejun
Hi all, I've read some earlier posts in the forum about replica exchange combined with umbrella sampling but still not sure if the restrain potential defined in the pull code will be included in the exchange criterion: P(i<->j) = min (1, exp[ (beta_i-beta_j)*(U(Ri, Dj) + U(Rj,Di) - U(Ri,Di) -

[gmx-users] Problem building Gromacs-4.5.5 on BlueGene/Q

2012-11-06 Thread Lin, Dejun
Hi all, I'm trying to build the mdrun binary for the BGQ system with the following commands (current dir is /scratch/dlin13/gromacs/gromacs-4.5.5/backend) : ../configure --prefix=/scratch/dlin13/gromacs/gromacs-4.5.5/backend \ --build=powerpc64-bgq-linux \ --enable-bl

[gmx-users] Force evaluation in umbrella pulling with nonzero pull_rate

2011-08-09 Thread Lin, Dejun
Hi, I'm trying to use umbrella pulling to do a targeted MD and I have the following pull code: pull= umbrella pull_geometry = distance pull_dim= N N Y pull_start = no pull_ngroups = 1 pull_group0 = REF pull_group1 = PULL pull_init1

RE: [gmx-users] To get PMF using pull geometry of cylinder

2011-05-26 Thread Lin, Dejun
Subject: Re: [gmx-users] To get PMF using pull geometry of cylinder Lin, Dejun wrote: > Ah...Sorry if I confused you. Actually what I meant is if I set the pull > code, e.g., as: > pull_geometry = position > pull_dim = N N Y > pull_rate1 = 0.1 > pull_init1 = 3.0 > pull_vec1 = 0 0 1

RE: [gmx-users] To get PMF using pull geometry of cylinder

2011-05-26 Thread Lin, Dejun
-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul [jalem...@vt.edu] Sent: Thursday, May 26, 2011 11:26 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] To get PMF using pull geometry of cylinder Lin, Dejun wrote: > Thank you Justin. But I'm s

RE: [gmx-users] To get PMF using pull geometry of cylinder

2011-05-26 Thread Lin, Dejun
o get PMF using pull geometry of cylinder Lin, Dejun wrote: > Hi all, > > I want to do an umbrella sampling to calculate the potential of mean force of > a micelle fusing to a lipid membrane. In the starting configuration, the > membrane normal is set in z direction and the membrane is under

[gmx-users] To get PMF using pull geometry of cylinder

2011-05-25 Thread Lin, Dejun
Hi all, I want to do an umbrella sampling to calculate the potential of mean force of a micelle fusing to a lipid membrane. In the starting configuration, the membrane normal is set in z direction and the membrane is under the micelle (z(COM-membrane) < z(COM-micelle)). At the beginning, I used