Re: [gmx-users] coarse-grained model of POPC in Martini coarse-grained force field?

POPC lipid is defined in the lipid itp file you'll find on the website. http://md.chem.rug.nl/cgmartini/index.php/forcefield-parameters/56-lipids POPC coordinate file is indeed not present on the website. However, transforming a DOPC or DPPC coordinate file to a POPC coordinate file goes only b

[gmx-users] coarse-grained model of POPC in Martini coarse-grained force field?

I'd like to run simulations with coarse grained model lipid bilayer.  I can not  find the force field for coarse grain POPC lipid or equilibrated bilayer coordinates in Martini website. Please help me! thank you! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs

[Fwd: Re: [gmx-users] coarse-grained model]

Hi, Dongsheng By checking mdlib/force.c, it is indeed that only one 1-4 table is read. David, would you like to give some clue in adding support for multiple 1-4 tables? Regards, Yang Ye Original Message Subject:Re: [gmx-users] coarse-grained model Date: Thu, 13

Re: [gmx-users] coarse-grained model

Yang Ye, Thank you for your help! I can use the table without any complaint, but I get all zeros for LJ and LJ14. I believe something is wrong. The following is from my log file: Table routines are used for coulomb: FALSE Table routines are used for vdw: TRUE Cut-off's: NS: 1.4 Coulomb:

Re: [gmx-users] coarse-grained model

Dongsheng Zhang wrote: Yang Ye, I am sorry to tell you I am not clear yet. Do you think I need to specify energygrps and corresponding energygrp_table? If so, then I got any error message. gp1 includes atom A, and gp3 includes atom A and B. Gromacs will complain that atoma has been in two gro

Re: [gmx-users] coarse-grained model

Yang Ye, I am sorry to tell you I am not clear yet. Do you think I need to specify energygrps and corresponding energygrp_table? If so, then I got any error message. gp1 includes atom A, and gp3 includes atom A and B. Gromacs will complain that atoma has been in two groups. Each group uses it ow

Re: [gmx-users] coarse-grained model

Don't worry about that. mdrun -tablep {tablep} will follow the scheme {tablep}_A_A.xvg, {tablep}_B_B.xvg ... {tablep} may be replaced by your own filename. Yang Ye Dongsheng Zhang wrote: Yang ye, Thank you very much. I have three different monomers in my system, so I have 6 different regula

Re: [gmx-users] coarse-grained model

Yang ye, Thank you very much. I have three different monomers in my system, so I have 6 different regular VMDs and 6 different 1-4 interactions. Could you please tell me how to organize those table.xvg files? energygrps = gp1 gp2 gp3 gp4 gp5 gp6 ... gp12 energygrp_table = A A B B C C A B A C B C

Re: [gmx-users] coarse-grained model

mdrun -tablep Dongsheng Zhang wrote: Hello, GMX users, I have a coarse-grained model. Both 1-4 and regular vdw interaction are tabulated, but no electrostatic interaction. Since there is no entry for 1-4 interaction in energy_table. I am thinking to fool gromacs by treating 1-4 interactions as

[gmx-users] coarse-grained model

Hello, GMX users, I have a coarse-grained model. Both 1-4 and regular vdw interaction are tabulated, but no electrostatic interaction. Since there is no entry for 1-4 interaction in energy_table. I am thinking to fool gromacs by treating 1-4 interactions as electrostatic interactions, in other wor