[gmx-users] PG/PE 3:1 lipid bilayer

Hello all, I got the pre equilibrated POPE/POPG 3:1 bilayer from http://www.softsimu.net/downloads.shtml While introducing the peptide to it found error with AtomTypes. I am using charmm36-mar2014.ff. How to solve this? Thanks in advance -- Gromacs Users mailing list * Please search the

Re: [gmx-users] CHARMM36 force field available for GROMACS

Hi Justin and Roland, we are interested in simulating a glycosilated protein. We already have a pdb file (and psf topology) with the charmm/namd format/nomenclature. We managed to have pdb2gmx read the carbohydrate residues by adding the relative entries in the residuetypes.dat, however we have

Re: [gmx-users] CHARMM36 force field available for GROMACS

On 4/10/14, 2:51 AM, gsettanni wrote: Hi Justin and Roland, we are interested in simulating a glycosilated protein. We already have a pdb file (and psf topology) with the charmm/namd format/nomenclature. We managed to have pdb2gmx read the carbohydrate residues by adding the relative

Re: [gmx-users] free energy caculation error

Hi Justin, thank you very much! according to your advise, my error is solved successfully. -- View this message in context: http://gromacs.5086.x6.nabble.com/free-energy-caculation-error-tp5015758p5015783.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. --

[gmx-users] the result of the free energy

Hi all, when i calculate the free energy of a molecule, the result is as the picture . i do not understand the true meaning. what is the relationship between dH/d(lambda) the .xvg file got and the free energy ? and what is the meaning of the lambda ? thank you in advance. -- View this message in

[gmx-users] (no subject)

-- New ideas, fragile as spring flowers, easily bruised by the tread of the multitude, may yet be cherished by the solitary wanderer., Fred Hoyle, *The Black Cloud*. Everybody knows that something can't be done until somebody turns up who doesn't know that it can't be done and he does it.,

[gmx-users] the result of the free energy

Hi all, when i calculate the free energy of a molecule, the result is as the picture . i do not understand the true meaning. what is the relationship between dH/d(lambda) the .xvg file got and the free energy ? and what is the meaning of the lambda ? thank you in advance.

Re: [gmx-users] the result of the free energy

On 4/10/14, 10:40 AM, jane wrote: Hi all, when i calculate the free energy of a molecule, the result is as the picture . i do not understand the true meaning. what is the relationship between dH/d(lambda) the .xvg file got and the free energy ? and what is the meaning of the lambda ? thank you