[gmx-users] residue IDs are not ordered in gro file.

Hi, there: I found that in gromacs version 4.5.1, the residue ids are not ordered consecutively as before in the .gro file. For example, if I have two chains in the protein, then the residue ids will be ordered with respect to each individual chain, rather than reordered to be a complete

[gmx-users] Energy Minimzation with Gromacs leads to distortion of planar groups

Dear Gmxusers, I have noticed that energy minimization with gromacs (gromos G53a6 forcefield) had led to the distortion of sidechain planarity in my protein model. Comparison of PROCEHCK results between the pre- and post energy minimized structures have shown an increase in the number of distor

Re: [gmx-users] pulling experiment

Xiaohua Zhang wrote: Sorry for my mistake about the group names. I was confused just to find it difficult to simultaneously fix one group (layer0) but pull another (layer2). It is possible to fix an absolute reference and pull layer2, but layer0 might follow the motion of layer2. For such e

Re: [gmx-users] pulling experiment

Xiaohua Zhang wrote: Dear gmx-users I want to design such kind of computer experiment: For a system composed of non-bonded three layers (carbon nanotubes, graphene, or whatever), I want to fix layer0 (the group name) to exactly (0,0,0), and pull layer2 by a constant force, for example, alon

Re: [gmx-users] pulling experiment

Sorry for my mistake about the group names. I was confused just to find it difficult to simultaneously fix one group (layer0) but pull another (layer2). It is possible to fix an absolute reference and pull layer2, but layer0 might follow the motion of layer2. For such experiment, the relative spee

[gmx-users] pulling experiment

Dear gmx-users I want to design such kind of computer experiment: For a system composed of non-bonded three layers (carbon nanotubes, graphene, or whatever), I want to fix layer0 (the group name) to exactly (0,0,0), and pull layer2 by a constant force, for example, along positive x all the time.

Re: [gmx-users] g_cluster cutoff

Shalom Andreas, I suggest you would look into the RMSD distribution inside your clusters (file namermsd-dist.xvg). In this file you will see one or more peak. The cut off you use should be larger then this peak but smaller then the second peak. I know this is a bit simplicity, but for more

Re: [gmx-users] g_cluster cutoff

I'm not sure this is necessarily the case. Have you tried other methods (gromos for example)? What are you getting when using other methods? Regards, -Shay On Fri, Sep 17, 2010 at 6:14 PM, Kukol, Andreas wrote: > Hi, > > I am using g_cluster to analyse a trajectory (protein backbone): > > g_clus

Re: [gmx-users] bug in function read_next_vmd_frame

Hi, thanks a lot. You are right. Fixed in GIT. Thus will be fixed in 4.5.2. This bug affects reading a non-GROMACS trajectory format (e.g. DCD) with a non-symmetric box (box vector B!=C). Roland On Sun, Sep 19, 2010 at 3:05 PM, BIN ZHANG wrote: > Hi, there: > > It seems to me that there was a

[gmx-users] bug in function read_next_vmd_frame

Hi, there: It seems to me that there was a bug at line 214 of function read_next_vmd_frame() in file ./src/gmxlib/vmdio.c. vec[0] = .1*ts.A; vec[1] = .1*ts.B; vec[2] = .1*ts.B; should be changed to : vec[0] = .1*ts.A; vec[1] = .1*ts.B; vec[2] = .1*ts.C; This is identified in gromacs4.5.1 ve

[gmx-users] cubic spline and continuous derivatives

Hello, The gromacs manual states that for cubic spline interpolation of potential energy and forces, "V and V’ are continuous, while V” is the first discontinuous derivative." This makes sense to me as there is a unique solution for parameters A2 and A3 if V and V' to the left and right are giv