[gmx-users] Shell dynamics with vdW terms.

Hello, I have some troubles understanding the way used by Gromacs in optimizing the position of shells. In section 3.5.1 the manual says that the force on a shell particle is decomposed into two terms. The first represents the polarization and the second includes the Coulomb and van der Waals

RE: [gmx-users] Shell dynamics with vdW terms.

Hi, The equation you refer to is only an initial guess for the optimization. The positions of the shells are optimized using the forces from the full potential function. Berk > From: raf...@us.es > To: gmx-users@gromacs.org > Date: Tue, 9 Jun 2009 09:51:13 +0200 > Subject: [gmx-users] Shell dyn

Re: [gmx-users] problem in running grompp

--- On Mon, 8/6/09, Justin A. Lemkul wrote: From: Justin A. Lemkul Subject: Re: [gmx-users] problem in running grompp To: "Discussion list for GROMACS users" Date: Monday, 8 June, 2009, 4:47 PM Samik Bhattacharya wrote: > hi > i am simulating a membrane protein in POPC bilayer and for that

Re: [gmx-users] problem in running grompp

Samik Bhattacharya wrote: Thank you Justin for the answar. but now how to solve it? where should i make changes to correct that? pls let me know what to do... waiting for your answar Thank you again.. "CA" is not an alpha-carbon, it is a ffgmx atom type. So, therefore, y

[gmx-users] trouble for old/new GROMACS site

Hi all, probably this is a very trivial question: how can I find information in the GROMACS site? I'm quite in trouble because I'm trying to search for some information in the gmx-user archive, and I can't reach it neither in the old GROMACS site nor in the new one. I supposed I had to register t

Re: [gmx-users] trouble for old/new GROMACS site

Anna Marabotti wrote: Hi all, probably this is a very trivial question: how can I find information in the GROMACS site? I'm quite in trouble because I'm trying to search for some information in the gmx-user archive, and I can't reach it neither in the old GROMACS site nor in the new one. I su

Re: [gmx-users] Shell dynamics with vdW terms.

On Tuesday 09 June 2009 10:02:47 Berk Hess wrote: > Hi, > > The equation you refer to is only an initial guess for the optimization. > The positions of the shells are optimized using the forces from > the full potential function. > > Berk > > > From: raf...@us.es > > To: gmx-users@gromacs.org > > D

RE: [gmx-users] Shell dynamics with vdW terms.

> From: raf...@us.es > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] Shell dynamics with vdW terms. > Date: Tue, 9 Jun 2009 16:29:39 +0200 > > On Tuesday 09 June 2009 10:02:47 Berk Hess wrote: > > Hi, > > > > The equation you refer to is only an initial guess for the optimization. > > Th

[gmx-users] units of eigenvalues of mass-weighted covariance matrix

Dear all, I am confused on the units of the eigenvalues calculated from g_covar of mass-weighted covariance matrix. From the output, it says the unit is "(nm\S2\N)" but from my understanding, it is supposed to be kg/m2. Thanks for advance for any comments. Regards, Qin ___

[gmx-users] non-standard residues in pdb2gmx

Hey everyone, I have a .pdb file that I need to convert to .gmx. The tricky thing is that the protein has a lipid bound to the N-terminus, which pdb2gmx doesn't recognize. The lipid is a myristic acid residue (14:0), and I haven't been able to find it in any database. What would be the most stra

Re: [gmx-users] non-standard residues in pdb2gmx

Gard Nelson wrote: Hey everyone, I have a .pdb file that I need to convert to .gmx. The tricky thing is that the protein has a lipid bound to the N-terminus, which pdb2gmx doesn't recognize. The lipid is a myristic acid residue (14:0), and I haven't been able to find it in any database. W

Re: [gmx-users] units of eigenvalues of mass-weighted covariance matrix

Wang Qin wrote: Dear all, I am confused on the units of the eigenvalues calculated from g_covar of mass-weighted covariance matrix. From the output, it says the unit is "(nm\S2\N)" but from my understanding, it is supposed to be kg/m2. Various of the GROMACS analysis tools don't write t

Re: [gmx-users] non-standard residues in pdb2gmx

Hi, > What might be even easier is to create an .itp file for myristic acid, so > you can #include "myristic.itp" in any topology that needs it.  That way you > don't have to mess with .rtp files, or run pdb2gmx for every system that > contains myristic acid. But this doesn't help when it has to

Re: [gmx-users] Shell dynamics with vdW terms.

On Tuesday 09 June 2009 18:27:16 Berk Hess wrote: > > From: raf...@us.es > > To: gmx-users@gromacs.org > > Subject: Re: [gmx-users] Shell dynamics with vdW terms. > > Date: Tue, 9 Jun 2009 16:29:39 +0200 > > > > On Tuesday 09 June 2009 10:02:47 Berk Hess wrote: > > > Hi, > > > > > > The equation yo

Re: [gmx-users] units of eigenvalues of mass-weighted covariance matrix

Hi, Well, as has been pointed out before nm\S2\N stands for nm superscript 2 normal. That is correct for non mass-weigthed covariance analysis. It's just fluctuation. Why would it be kg/m2 (kg/nm2) for mass weighted? Look at the equations in the manual. It's sqrt(mass)*sqrt(mass)*nm*nm, which make