[gmx-users] Re: FEP + Ham. REMD

Have anybody been constructing virtual sites for calculating PMF via FEP? 2013/4/6 Yuri Garmay > Hi all! > > I have a problem. So as it can be seen in the theme I am trying to improve > sampling of free energy calculating simulation by using replica exchange. > In the gmx4.6 it

[gmx-users] FEP + Ham. REMD

Hi all! I have a problem. So as it can be seen in the theme I am trying to improve sampling of free energy calculating simulation by using replica exchange. In the gmx4.6 it is simple while using FEP technique, but does not implemented for umbrella sampling. But I want evaluate potential of mean f

Re: [gmx-users] LINCS crushes

> > Try minimizing again now with all bonds constrained using the output of > the EM that ran. Generally, if EM crashes, your system contains some > unresolvable clash or inappropriate geometry. Perhaps you have now relaxed > the bad interactions sufficiently to proceed. > I had examined struct

[gmx-users] LINCS crushes

Hi, all! I am trying to simulate a system of peptide, water, NaCl and DMSO. I used pdb2gmx to generate .top file for DMSO and then created this .itp: (initial DMSO structure had been minimized before it was used for box generation) [ moleculetype ] ; Namenrexcl DMSO 3 [

Re: [gmx-users] Re: g_covar

There is similar question in the mail list: http://www.mail-archive.com/gmx-users@gromacs.org/msg41737.html Regards, Yuri 2011/8/16 גדעון לפידות > Thanks for your replies. > I would like to clarify regarding my first questionn. I don't want a g_dist > matrix. I would like to get a covariance ma

Re: [gmx-users] g_covar

Hi Tsjerk. What do you mean with mean? Mean without fitting is a single point. > Mean only makes sense after aligning. Now there's a nice recursive > problem: > 1. Calculate mean to get reference > 2. Align to reference to calculate mean I mean the limit of this sequence is mean) Because it is n

Re: [gmx-users] g_covar

I know, but the best reference is "mean". And it is another mean that calculated after fit at some frame. 2011/8/16 Tsjerk Wassenaar > Hi, > > > This questuion may be hard. You need rabbi's advice)) > > But there are some feature of the reference structure that makes it good > or > > bad. It is

Re: [gmx-users] g_covar

Hi. > Second, Say I would like to analyze the main difference between two > trajectories of the same protein using PCA. is it KOSHER to use the same > first frame which is identical between both runs as the reference strucutre > and then just append both runs into a single trajectory and then use

Re: [gmx-users] em ok, md wrong

2009/10/28 Liliya Shamova > Hi everybody! > Dihedrals seem be incorrect. Check it. (I don't know what have to be, is it planar molecule or not, it have be known, but it seems to be incorrect, as you say molecule distorted) Additionally, you should use improper dihedrals for making planar parts.