Re: [gmx-users] gromos parameterisation in OPLS

If you include in the .itp file all the necessary combinations in those sections, then yes, the .itp file is reasonable and will use the OPLS-AA parameters for those specified items. Take care to get the numbering right after that point, because you will likely be inserting lots of hydrogens!

Re: [gmx-users] Re[4]: g_msd vs g_velacc. [SOLVED]

Vitaly Chaban wrote: >> I've got a discrepancy calculating the diffusion coefficient via >> Green-Kubo equation and via Einstein equation. >> > > >> $ g_velacc -nonormalize -acflen 1001 >> $ g_analyze -f vac.xvg -integrate >> Do I miss any important keyword here? It seems the result of int

[gmx-users] regarding trjconv

Dear all, RMSD and RMSF of my protein is showing abnormal flucutuation. To overcome this problem I am using following commands--> trjconv -f *.trr -o trajout_whole.xtc -s *.tpr -pbc whole trjconv -f trajout_whole.xtc -o trajout_nojump .xtc -pbc nojump

Re: [gmx-users] gromos parameterisation in OPLS

can i put the partial charges from Gaussian? --- On Tue, 17/6/08, Justin A. Lemkul <[EMAIL PROTECTED]> wrote: > From: Justin A. Lemkul <[EMAIL PROTECTED]> > Subject: Re: [gmx-users] gromos parameterisation in OPLS > To: [EMAIL PROTECTED], "Gromacs Users' List" > Date: Tuesday, 17 June, 2008, 4:

Re: [gmx-users] gromos parameterisation in OPLS

Parameterization should always be done according to the derivation of the original force field. I don't know all the specifics of the OPLS-AA parameterization, so you'll have to look into it. -Justin ANINDITA GAYEN wrote: can i put the partial charges from Gaussian? --- On Tue, 17/6/08, Jus

Re: [gmx-users] Re[4]: g_msd vs g_velacc. [SOLVED]

Florian Dommert wrote: > Vitaly Chaban wrote: > > >>> I've got a discrepancy calculating the diffusion coefficient via >>> Green-Kubo equation and via Einstein equation. >>> >>> >> >> >>> $ g_velacc -nonormalize -acflen 1001 >>> $ g_analyze -f vac.xvg -integrate >>> Do I mis

Re: [gmx-users] gromos parameterisation in OPLS

On Tue, 17 Jun 2008 17:31:53 +0530 (IST) ANINDITA GAYEN <[EMAIL PROTECTED]> wrote: can i put the partial charges from Gaussian? In principle you can do everything assuming that it is justified. Putting charges from Gaussian do not mean much. It sounds very elaborated because Gaussian could i

[gmx-users] Re[5]: g_msd vs g_velacc. [SOLVED]

> I thought the flag -mol > calculates > the momentum autocorrelation function, so in my opinion the result has > to be divided > by the square of the masses of the molecules to obtain the diffusion > constant. Flo, you're completely right. Sorry for my mistake as for normalization here. -- Vita

Re: [gmx-users] gromos parameterisation in OPLS

On Tue, Jun 17, 2008 at 02:21:09PM +0200, Xavier Periole wrote: > On Tue, 17 Jun 2008 17:31:53 +0530 (IST) > ANINDITA GAYEN <[EMAIL PROTECTED]> wrote: > > > > > >can i put the partial charges from Gaussian? > In principle you can do everything assuming that it is justified. > > Putting charges fr

Re: [gmx-users] regarding trjconv

Anamika Awasthi wrote: Dear all, RMSD and RMSF of my protein is showing abnormal flucutuation. To overcome this problem I am using following commands--> trjconv -f *.trr -o trajout_whole.xtc -s *.tpr -pbc whole trjconv -f trajout_whole.xtc -o trajout_nojump .

[gmx-users] regarding rmsd !!

Dear All, My protein is simulating for 20 ns and 16 ns has already over, but I want to analyze RMSD and RMSF for this 16 ns simulation, without stopping the running simulation.it was crashed before, so I used tpbconv -f previous.trr -e previous.edr -s previous.tpr -o new.tpr -until 2 t

Re: [gmx-users] regarding rmsd !!

Check your input/output! In this case it seems you are missing/forgetting the -s flag to specify the name of the tpr-file. /Per 17 jun 2008 kl. 17.07 skrev Anamika Awasthi: Dear All, My protein is simulating for 20 ns and 16 ns has already over, but I want to analyze RMSD and

Re: [gmx-users] regarding rmsd !!

I would also suggest to use the xtc and not the trr file for analysis. The (compressed) xtc is usually written more often than the (full-precision) trr. Jochen Anamika Awasthi wrote: Dear All, My protein is simulating for 20 ns and 16 ns has already over, but I want to analyze RMSD

Re: [gmx-users] Position Constraint

Check the "real posres(..." routine in src/gmxlib/bondfree.c Jochen Jae Hyun Park wrote: Dear GROMACS users, I would like to modify the source code on the position restraint part (restraining the atoms in a protein using -DPOSRES). Could anybody let me know where (or which subroutine) I can

[gmx-users] RMSD graph

Dear All, Please tell, what should I predict from this graph? I can understand this is normal type of graph. Sorry for inconvenience, but I want to ask some questions, my this job crashed many time, because of power shut down and I had to restart this again and again, I used tp

Re: [gmx-users] regarding rmsd !!

Jochen Hub wrote: I would also suggest to use the xtc and not the trr file for analysis. The (compressed) xtc is usually written more often than the (full-precision) trr. Well, if the user set it up that way. If they have done so, they they should be able to remember which is better for their

Re: [gmx-users] RMSD graph

Anamika Awasthi wrote: Dear All, Please tell, what should I predict from this graph? We can't tell from your graph what's happening because you haven't told us how you generated it. It's also not our job to do so - it's yours. You can go at look at your data at the points that have "

Re: [Bulk] [gmx-users] RMSD graph

Quite likely, it is due to part of molecule moving "out of box". Also, the molecule could be of multiple chain. So you need to find a way to put the whole molecule in one piece. Try various options from trjconv -pbc. If it is DNA, a trick is to define one chain as an index group and then cente