[gmx-users] fitting dihedral angle function parameters using gromacs

2010-01-23 Thread fay4
Dear Gromacs developer: I am asking for your help about fitting a dihedral angle parameters using gromacs md simulation. One article (link: http://www.mpip-mainz.mpg.de/~andrienk/journal_club/opls.pdf) says that fitting a dihedral angle potential parameters needs three steps: 1) perform ab initio

[gmx-users] PMF

2010-01-23 Thread leila karami
Hi How Potential of Mean Force (PMF) is calculated by gromacs? what command? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests t

Re: [gmx-users] About "Apply Multiple bonded interactions" for dihedral potential definition

2010-01-23 Thread Justin A. Lemkul
WU Yanbin wrote: Hi, all, According to Manual v3.3, "It's possible to apply multiple bonded interactions of the same type on the same atoms" [12th line of Page 98]. If a dihedral potential for 4 neighboring atoms is defined 3 times using the "periodic type" in the topology file, like V=k1*(

Re: [gmx-users] PMF

2010-01-23 Thread Justin A. Lemkul
leila karami wrote: Hi How Potential of Mean Force (PMF) is calculated by gromacs? what command? Calculating the PMF is not a command, but rather a somewhat extensive simulation procedure that will depend upon the quantity you want to measure (binding energy of a ligand, PMF of rotating

[gmx-users] New tutorial available - umbrella sampling

2010-01-23 Thread Justin A. Lemkul
Hi all, I've been working on an umbrella sampling/PMF tutorial for some time now, and I have just added it to the Tutorials page on the Gromacs site. As with my previous tutorials, I would welcome anyone to look through it and give me any feedback you may have on making it better; feel free

[gmx-users] fitting dihedral angle function parameters using gromacs

2010-01-23 Thread chris . neale
I have never done this myself. Nevertheless, I'm going to take a shot since you haven't got an answer yet. Dihedral parameters can be thought of as consistently developed fudge factors that are used to fine-tune a parameter set. The word consistent here implies that there is a method to dev

Re: [gmx-users] fitting dihedral angle function parameters using gromacs

2010-01-23 Thread fay4
Dear Mr. Chris: Thanks for your reply! I will try your method! best regards, fangyong > I have never done this myself. Nevertheless, I'm going to take a shot > since you haven't got an answer yet. > > Dihedral parameters can be thought of as consistently developed fudge > factors that are used

[gmx-users] Re: Re: Fw: Re: Polymer-protein problem

2010-01-23 Thread P.R.Anand Narayanan
Dear Sir, I energy optimised the polymer-protein structure using HYPERCHEM. The moment I created peptide bonds between them, the pdb was saved like the format mentioned previously. for eg; HETATM1 N 1-24.998 12.703 12.925 > > HETATM2 C 2-24.749 12.813 11.

[gmx-users] gas adsorption on CNT

2010-01-23 Thread leila karami
Hi,I want to simulate gas adsorption on finite CNT. Does CNT be flexible or rigid? which is better? 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/search before posting! Please don

[gmx-users] Weird error message from QM/MM run.

2010-01-23 Thread yoochan,myung
QM/MM calculation requested. there we go! Layer 0 nr of QM atoms 30 QMlevel: RHF/STO-3G number of CPUs for gaussian = 1 memory for gaussian = 5000 accuracy in l510 = 8 NOT using cp-mcscf in l1003 Level of SA at start = 0 [yoochancal2-desktop:09740] *** Process received signal *** [yoochancal2-

Re: [gmx-users] Re: Re: Fw: Re: Polymer-protein problem

2010-01-23 Thread Mark Abraham
On 24/01/10 18:02, P.R.Anand Narayanan wrote: Dear Sir, I energy optimised the polymer-protein structure using HYPERCHEM. The moment I created peptide bonds between them, the pdb was saved like the format mentioned previously. for eg; HETATM 1 N 1 -24.998 12.703 12.925 > > HETATM 2 C 2 -24.749

Re: [gmx-users] gas adsorption on CNT

2010-01-23 Thread Mark Abraham
On 24/01/10 18:16, leila karami wrote: Hi,I want to simulate gas adsorption on finite CNT. Does CNT be flexible or rigid? which is better? thanks ... whichever models the real conditions better. The only way we'd know would be by doing such work or reading about such work. Either way, you'