[gmx-users] Tensor of inertia moments at each time step

Hi, Is it possible in GROMACS to extract from trajectory file 9 components of tensor of inertia moments at each time step? I know that it is possible to extract 3 vectors, but not whole tensor. Any suggestions? Thank you Egis --- On Tue, 12/1/09, gmx-users-requ...@gromacs.org

[gmx-users] topology of HEO compound in .rtp for G96 ff

Hello, could anyone help me and check if the topology of the HEO compound was done properly for G96 ff? Thanks in advance. I couldn't find it in the database, so I decided to try to make it manualy. Any comments would be appreciated. Or maybe does exists any programs who does the work? [ HEO

[gmx-users] crash on Source code file: nsgrid.c, line: 226

Dear developers, I have got this message on the crash (system with 192 molecules, paralellipiped)   --- Program mdrunmpi, VERSION 3.3 Source code file: nsgrid.c, line: 226 Range checking error: Explanation: During neighborsearching, we assign

[gmx-users] a huge topology parameter c1 (angles)

24 26 2 120.0 505.0 120.0 505.0 ; HAE CAE CAI 16 26 24 2 120.0 505.0 120.0 505.0 ; CAR CAI CAE Thanks Egidijus Kuprusevicius Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. ___ gmx-users mailing listgmx

[gmx-users] Lincs error and explosion of the system

gen_temp = 299 gen_seed = 173529 Could anyone help me? Thanks Egidijus Kuprusevicius Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org

[gmx-users] segmentation fault (wrong settings in mdp file)

Dear All, maybe anyone knows why I'm getting a 'segmentation fault' error while I'm running mdrun. I know that something is wrong with my mdp file, but do not know what exactly can cause it (what parameters I should do not use or use instead). Thank you in advance

[gmx-users] problems in rtp while runing pdb2gmx

Dear all, could anybody know how to tackle the problem? I have such pdb file HETATM 1 CB1 DRG 1 -5.058 1.624 -0.274 1.00 C HETATM 2 HB11 DRG 1 -4.785 2.632 0.071 1.00 H HETATM 3 HB12 DRG 1 -6.149 1.562 -0.397 1.00 H HETATM 4 HB13 DRG 1 -4.568 1.422 -1.238 1.00 H HETATM 5 CG1 DRG 1

[gmx-users] error in .gro file

Dear all, I have tried to avoid using pdb2gmx and created manualy gro file and included my own itp in top file (itp file is the same as that who was included in rtp (in previous message 'error in rtp file')). I still having an error:

[gmx-users] Re: how to create tpr file from pdb created with Hyperhem for using with OPLS

Thanks Mark, but your first answer didn't help me at all. I want to create pdb manually which will work with gromacs pdb2gmx comand in order to get gro and top using OPLS, and seeking for some clues. It doesn't matter if it is Hyperchem or JME or MOL, I need a proper pdb which will be

[gmx-users] how to create tpr file from pdb created with Hyperhem for using with OPLS

Dear Gromacs developers, I have some very simple questions on how to get the file (tpr) wich could be run on Gromacs (MD). With Hyperhem I have drawn the target molecule, I obtained ent file containing ATOM and CONNECT sections: 1) What should I change in this ent file to be able to run this

[gmx-users] Re: gmx-users Digest, Vol 45, Issue 60

Thanks Mark, but your first answer didn't help me at all. I want to create pdb manually which will work with gromacs pdb2gmx comand in order to get gro and top using OPLS, and seeking for some clues. It doesn't matter if it is Hyperchem or JME or MOL, I need a proper pdb which will be

[gmx-users] on pdb files structure

Thank you for replies. Below there are pdb file format specifications. http://www.wwpdb.org/documentation/format23/sect9.html#HETATM Are these valid for Gromacs pdb files as well? What sections are important and should be present and what can be spared? Egidijus

[gmx-users] how to run MD of a new molecule using OPLS

Hi, Could anyone tell me how to parameterize a new molecule for using it with OPLS (basic principles). What a .pdb file should look like and what .mdp variables are specificaly related to OPLS? Thank you in advance Egidijus - Never miss a