[gmx-users] henry constant

Hello, I want to calculate the henry constant for a soluble gas in a solvent. For that, I use the tool -fee in g_energy to get deltaG. Is that the excess chemical potential, with which I can calculate the henry constant? Or is it not possible to calculate the henry-constant with this tool? Reg

Re: [gmx-users] query against box collapsed in case of tightly bound ligand

devawati dutta wrote: Dear Sir, Thank you for your suggestion regarding coulomb type and LIE method. I have successfully done the job. But now I am facing another type of problem. I am performing simulation of a protein ligand complex where the ligand is si

Re: [gmx-users] Nitrogen box

sarah k wrote: dear users, I want to use Nitrogen as my solvent. How can I prepare the box and compile the *.gro file? Please, guide me in detail. Thanks in advance! Make a coordinate file for a single N2 molecule (should be really easy) and use either genconf -nbox or genbox -ci -nmol

[gmx-users] query against box collapsed in case of tightly bound ligand

Dear Sir, Thank you for your suggestion regarding coulomb type and LIE method. I have successfully done the job. But now I am facing another type of problem. I am performing simulation of a protein ligand complex where the ligand is sitting deep inside the grrove o

[gmx-users] Nitrogen box

dear users, I want to use Nitrogen as my solvent. How can I prepare the box and compile the *.gro file? Please, guide me in detail. Thanks in advance! Regards, Fatemeh Keshavarz -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search t

Re: [gmx-users] Fwd: Enquire about double strand DNA in gmx 4.5.3 charmm27 ff.Thank you.

On 2011-02-26 10.27, David van der Spoel wrote: I found your comments in gmx-user communications. I’m using gmx 453, with DNA system. Pdb2gmx is ok, but gmx treated each string as protein. I used command pdb2gmx -f new.pdb -o wt.gro -p wt.top -water tip4p then choose charmm27 ff, everything l

[gmx-users] Fwd: Enquire about double strand DNA in gmx 4.5.3 charmm27 ff.Thank you.

I found your comments in gmx-user communications. I’m using gmx 453, with DNA system. Pdb2gmx is ok, but gmx treated each string as protein. I used command pdb2gmx -f new.pdb -o wt.gro -p wt.top -water tip4p then choose charmm27 ff, everything looks good. However I found during my md runs, DNA

[gmx-users] g_velacc -mol option

Dear Users, I am trying the calculate the velocity autocorrelation function of molecules. g_velacc has the -mol option. I would like to know/confirm how the velocity autocorrelation function of *molecules* is calculated. Is it calculated from the center of mass velocity of each of the molecules?