[gmx-users] Re: SD temperature coupling groups

Hey! I think Your problem is from function init_stochd in update.c (src/mdlib). When You set tau_t to 0 You got division by 0 on line 288: for(n=0; ndelta_t/ir->opts.tau_t[n]; sdc[n].eph = exp(sdc[n].gdt/2); sdc[n].emh = exp(-sdc[n].gdt/2); sdc[n].em = exp(-sdc[n].gdt); I t

[gmx-users] table_bonded.xvg

"table.xvg" and for a tabulated bond table number 0, it correctly opens "table_b0.xvg" Berk From: A.Rzepiela at rug.nl To: gmx-users at gromacs.org Date: Fri, 24 Oct 2008 13:45:53 +0200 Subject: [gmx-users] table_bonded.xvg Dear Users In gromacs 4.0, in file force.c in functio

[gmx-users] table_bonded.xvg

Dear Users In gromacs 4.0, in file force.c in function make_bonded_tables line (1007) sprintf(tabfn + strlen(basefn) - strlen(ftp2ext(efXVG)) - 1,"_%s%d.%s", tabext, i, ftp2ext(efXVG)); produces table_bonded_bonded.xvg instead of table_bonded.xvg Greetings Andrzej Rzepiela

[gmx-users] g_bond No distribution... error

Dear Users In the gmx_bond.c maximal distance ( 2 A ) between two bonded atoms is hardcoded ( lines 137: 141) if (blen == -1) { b0 = 0; b1 = 0.2; db = (b1-b0)/MAXTAB; } so if one wants to compute distribution for CG molecule, program cr

[gmx-users] Different results with and without constraints for pr coupling.

Dear all The system, 75 hexadecane molecules, when simulated with Parrinello-Rahman (isotropic), Nose-Hoover and option "constraints = none" is freezing. When constraints are changed to "constraints = all-bonds" (lincs), this is not observed ( temp is above melting point ). This behavi