[gmx-users] unit conversion

Hi, When I convert FF parameters from OPLS (in Gromacs) to Charmm, I divide bond and angle force constants, i.e., Kb and Ktheta, by 836.8 and 8.368. However, parameters for tip3p water do not convert properly in this ways. For example, Kb = 502416.0 kJ/mol/nm^2 for OW-HW in Gromacs and 450.0 kcal

[gmx-users] question regarding mutation from CH --> COH during free energy calculation

Hi, I sent the following email last Saturday and I haven't got any reply yet. I wonder whether you can suggest something regarding this issue. Thanks in advance. ** I edit my topology file for mutating CH --> C

[gmx-users] question regarding mutation from CH --> COH during free energy calculation

Hi, I edit my topology file for mutating CH --> COH during free energy calculation. Since one hydrogen atom attached to carbon disappears, while two O and H atoms are appearing, I build topology file as follows: 8 opls_169 1TESTO 3 -0.715.9994 opls_1400.1

Re: [gmx-users] question about energygrps

> > > On 5/12/13 1:53 PM, Hyunjin Kim wrote: >>> >>> >>> On 5/12/13 1:31 PM, Hyunjin Kim wrote: >>>>> >>>>> >>>>> On 5/12/13 1:14 PM, Hyunjin Kim wrote: >>>>>>> >>>>>&

Re: [gmx-users] question about energygrps

> > > On 5/12/13 1:31 PM, Hyunjin Kim wrote: >>> >>> >>> On 5/12/13 1:14 PM, Hyunjin Kim wrote: >>>>> >>>>> >>>>> On 5/12/13 12:54 PM, Hyunjin Kim wrote: >>>>>>> >>>>>>&g

Re: [gmx-users] question about energygrps

> > > On 5/12/13 1:14 PM, Hyunjin Kim wrote: >>> >>> >>> On 5/12/13 12:54 PM, Hyunjin Kim wrote: >>>>> >>>>> >>>>> On 5/12/13 2:25 AM, Hyunjin Kim wrote: >>>>>> Dear, >>>>>> >

Re: [gmx-users] question about energygrps

> > > On 5/12/13 12:54 PM, Hyunjin Kim wrote: >>> >>> >>> On 5/12/13 2:25 AM, Hyunjin Kim wrote: >>>> Dear, >>>> >>>> I want to calculate LJ and Electrostatic energies between two groups >>>> defined in inde

Re: [gmx-users] question about energygrps

> > > On 5/12/13 2:25 AM, Hyunjin Kim wrote: >> Dear, >> >> I want to calculate LJ and Electrostatic energies between two groups >> defined in index.ndx during rerun with original trajectory. >> >> The following is what I tried: >> >> 1. i

[gmx-users] question about energygrps

Dear, I want to calculate LJ and Electrostatic energies between two groups defined in index.ndx during rerun with original trajectory. The following is what I tried: 1. insert "energygrps r_1 r_25" in the test.mdp file. 2. grompp -f test.mdp -c x.gro -o x.tpr -p x.top -n index.ndx 3. mdrun -nt

[gmx-users] proper tau_t value with SD

Hi, Gromacs manual says that when "SD" used as a thermostat, an appropriate value for "tau_t" is 2 ps, since this results in a friction that is lower than the internal friction of water, while it is high enough to remove excess heat (unless cut-off or reaction-field electrostatics is used). Howeve

[gmx-users] number of molecules generated during pdb2gmx

Hi, I included a small organic moelcule using separating .itp and .rtp files in charmm36. If I ran pdb2gmx to generate top file, it generated properly. However, although I included 256 molecules, it still treated them as one molecule as follows: [ molecules ] ; Compound#mols Orgainic

[gmx-users] forgetten password

Hi, I forgot my password to access the mailing list site. What should I do to fix this? Thanks. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before postin

[gmx-users] grompp error with new format of angletypes

Dear, When I generated bond parameters as following and ran "grompp", then I had an error messages "No default Angle types" [ angletypes ] ; i j k functh0 cth ub0 cub OST CST OST 5 180.25104.0 0.0 0.0 CS SS FE 5