[gmx-users] Re: How to restrain dihedral angles to reserve the tacticity?

Dear Acharya, Thank you very much for this quick reply. According to your suggestion, I measure the main chain dihedral angles, only to find that same values are obtained for both isotactic and syndiotactic ones. Therefore, this way can not distinguish tacticity of polymer chains. For a good initia

[gmx-users] Re: about -return of mdrun

Dear gmxer's I employed the same gro and mdp files but different top files (only excl is different) for running previous and rerun mdrun with the generated frames. As I realize, the the rerun mdrun seems to restart one completely new mdrun which is not based on the previous frame. How to deal with

[gmx-users] Re: about -return of mdrun

Dear Justin, I am sorry to spell the word. In fact, I had referred to the -return as -rerun. Could you give me some another suggestion? Thank you very much! Chaofu Wu -- View this message in context: http://gromacs.5086.n6.nabble.com/about-return-of-mdrun-tp5004019p5004035.html Sent from the GR

[gmx-users] Re: difference between the tabulated and Cut-off Electicstatics potentials

Dear gmxers, Sorry to all that pays attention to my previous post. When I looked into the generated mdp files, I find that except the ele. potentials there is another difference in the running parameters, namely cut-off. Now I am sure that it is different cut-off that causes that big difference in

Re: [gmx-users] How to set up constraint distcance pulling

y much! On 6/7/12 7:38 AM, xiaowu759 wrote: >> Dear gmxers, >> I am performing COM pulling using GMX4.0.7, to obtain the PMF as a function >> of >> distance between the COMs of two molecules. However, quite strange resuluts >> are >> generated, i.e., t

[gmx-users] How to set up constraint distcance pulling

Dear gmxers, I am performing COM pulling using GMX4.0.7, to obtain the PMF as a function of distance between the COMs of two molecules. However, quite strange resuluts are generated, i.e., the distance can not be fixed at the value defined by pull_init1. The pull opinions are given below. Could

[gmx-users] constranit distance for pulling code

Dear gmxers, I have prepared the inputs and tried to run constraint distance pulling on two-molecule pair. However, one error is output which indicates that two atoms on the molecule including the pull group are beyond the 1-4 table range. I have chosen one reference group and one pull group. A

[gmx-users] calculation equation of g_vanhove

Dear gmxers, I try to use g_vanhove in the gmx, but I do not find what it actually calculates because no equations are put in the manual. By the definition, it seems to be a bit different from those in some articles. Could you please give it clearly? Thanks a lot for any reply! Dr. Chaofu Wu

[gmx-users] About g_vanhove

Dear gmxers, I want to analyze van Hove correlation function using g_vanhove in GMX. Is the calculated result self- or distinct part or total? I guess it is total. Then, can g_vanhove calculate separately the self and distinct parts? Please give me some hints. Thanks a lot for any replies. Best

[gmx-users] the density does not stablize

Dear gmxers, I try to perform NPT MD to obtain the density of system. But the value of density does not stablize even after over 40 ns. The content of mdp file can be seen below. How to deal with it? Please give me some hints. Thanks a lot for any replies. .mdp file: title

[gmx-users] Reorder of residues and atoms

Dear gmxers, While performing EM using GMX, I find in the resullting gro file, residues and atoms are reordered. Do this affect the simulation? Please give me some hints. Thanks a lot! Before EM，gro file: 1 HmP .. 2 HmP .. . 20 MmP ... 21 MmP .. .

[gmx-users] What does it mean by saying mca: base: component_find: unable to open....

Dear gmxers, We have installed gmx-4.5.4 on one cluster from the source, without any errors. I can also run mdrun in non-parallel way successful. However, when I run mdrun in parallel way as follows: mpimdrun -h some messages are given: [node10:03709] mca: base: component_find: unable to o

[gmx-users] Re: NPT issue in 4.0.7 and 4.5.3

Dear Moeed, You seem to be encountering same problem to mine, which was posted to this list, .titled "Unexpected results arising from T- and P-coupling methods". Some gmxers responded it. You can look for and see them. I wish they can be helpful to deal with your problem. Chaofu Wu, Dr.

[gmx-users] "Now there are 16 atoms. Deleted 304 duplicates."

Dear, As a small test, I want to simulate polystyene(PS) using GROMACS. Firstly, I obtain a pdb file of a PS chain consisting of 20 repeating unit(320 atoms totally ) and add the STY residues to the .rtp files. while running pdb2gmx, the procedure was finished "successfully". but I find that o