Re: [gmx-users] r_list and r_coulomb values while using PME

OZGE ENGIN wrote: So, using twin-range cut-off does not violate the energy conservation for RC method, but it violates for PME method. Is this the case ? twin range does not conserve energy with cutoff or RF either. however you must always compromise between accuracy and computational cost, t

Re: [gmx-users] Re: Measure contour area of bilayer undulation

Hi, > > > My point was rather the opposite - when people measure area/lipid in the > lab on bilayer slabs there will be undulations present since they are > typically not under tension. We discussed this with John Nagle a couple of > years ago, and came to the conclusion that you should not try

Re: Re: [gmx-users] r_list and r_coulomb values while using PME

So, using twin-range cut-off does not violate the energy conservation for RC method, but it violates for PME method. Is this the case ? -Original Message- From: David van der Spoel <[EMAIL PROTECTED]> To: Discussion list for GROMACS users Date: Sat, 01 Sep 2007 14:48:03 +0200 Subject: R

Re: [gmx-users] r_list and r_coulomb values while using PME

OZGE ENGIN wrote: 'The force is not the derivative of the potential', is it due to the types of calculations performed in PME, using of FFT for reciprocal sum? Because it does not matter while using reaction-field method. Sorry, this phenomenon is a little complicated to me :) this is only w

Re: Re: [gmx-users] r_list and r_coulomb values while using PME

'The force is not the derivative of the potential', is it due to the types of calculations performed in PME, using of FFT for reciprocal sum? Because it does not matter while using reaction-field method. Sorry, this phenomenon is a little complicated to me :) Thanks for your attention! Oz.

Re: [gmx-users] r_list and r_coulomb values while using PME

OZGE ENGIN wrote: Hi all, I can not understand why it is required to take same values for both r_list and r_coulomb parameters when using PME for calculation of electrostatic interactions? I read archieve, and gromacs manual. In archieve, similar question had been posted, but not replied ye

[gmx-users] r_list and r_coulomb values while using PME

Hi all, I can not understand why it is required to take same values for both r_list and r_coulomb parameters when using PME for calculation of electrostatic interactions? I read archieve, and gromacs manual. In archieve, similar question had been posted, but not replied yet. Thanks in advanc

RE: [gmx-users] charge density of lipid

I found one see this paper http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=1302891&blobtype=p df it is defined by sigma_M Best regards Yuguang Dr. Yuguang Mu Assistant Professor School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Tel: +65-63162

Re: [gmx-users] charge density of lipid

Mu Yuguang (Dr) wrote: No, net charge density estimated from experimental data. what does it mean, how is it measured? you can have nuclear charge minus electron density, but this is not very accurate. -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsal

RE: [gmx-users] charge density of lipid

No, net charge density estimated from experimental data. Best regards Yuguang -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of David van der Spoel Sent: Saturday, September 01, 2007 4:49 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] ch

Re: [gmx-users] charge density of lipid

Mu Yuguang (Dr) wrote: Dear all, How to estimate the charge density of a lipid , the reason we want to do is that we try a model system to mimic the lipid environment. It seems out of GROMACS discussion range, but I believe many Gromacs users do lipid simulations. do you mean electron dens

Re: [gmx-users] Fwd: what is the force function for proper dihedrals

[EMAIL PROTECTED] wrote: Haven't looked into the details yet, but this is worth noting for those interested. Thanks William. - Forwarded message from [EMAIL PROTECTED] - Date: Sat, 01 Sep 2007 00:15:25 -0400 From: William Noid <[EMAIL PROTECTED]> Reply-To: William Noid <[EMAIL P

[gmx-users] charge density of lipid

Dear all, How to estimate the charge density of a lipid , the reason we want to do is that we try a model system to mimic the lipid environment. It seems out of GROMACS discussion range, but I believe many Gromacs users do lipid simulations. Best regards Yuguang

[gmx-users] Re: Measure contour area of bilayer undulation

Hi, On Aug 31, 2007, at 11:02 PM, Hwankyu Lee wrote: Thank you very much for your suggestion in the gromacs forum, but I may not understand your explanation completely. In the small bilayer, there is no fluctuation, so area/lipid can be calculated based on the cell dimensions. But, in

Re: [gmx-users] Fullerene simulation

Hi Serdar, The gromacs mailing list gives a hit on fullerene from earlier this year. Also, a quick search on scholar.google.com (http://scholar.google.nl/scholar?q=fullerene+gromacs&hl=en&lr=&btnG=Search) also gives some hits. Tsjerk On 8/31/07, serdar durdagi <[EMAIL PROTECTED]> wrote: > Dear a

Re: [gmx-users] Correlation Matrix Calculation

Hi Arneh, Yes. As you should be able to recall, the (linear, not "generalized") correlation is formally given as: cor(x,y) = cov(x,y) / ( sqrt(var(x))*sqrt(var(y)) ) The diagonal elements of the covariance matrix give the variances... Cheers, Tsjerk On 8/31/07, Arneh Babakhani <[EMAIL PROTECT