[gmx-users] Announcing: Gromacs 4.0, release candidate 1

Stockholm, September 22 2008 In a bold move today, the Gromacs developers finally decided not to wait for Duke Nukem Forever before releasing Gromacs 4.0, and just put out release candidate 1 together with a new manual at ftp://ftp.gromacs.org:/pub/beta/ "We realize it could be a big disa

[gmx-users] Looking for polarizable and flexible water model

Dear gmx-users, For my simulations i'm looking for polarizable water model.  Shell models implemented in GMX are good-quality. But the question is that the model should be not only polarizable but also FLEXIBLE. To my present knowledge, there are only two alteratives. The first one is van Maar

Re: [gmx-users] Cann't get the same result ?

This is normal. You shall get statistical identical properties between runs. Besides obvious reasons (gen_vel=yes and gen_seed=-1, or optimize_fft=yes), there might be other factors. Regards, Yang Ye On 9/22/08 8:26 AM, xuji wrote: > Hi all: > I run mdrun of gromacs-3.3.3 6 times of a small simul

[gmx-users] lipidposre.itp file of popc

Yes, assuming that you include this file right after you define the lipid, and assuming that you meant to say CA1(51), and assuming that your lipid .itp has only a single molecule. You could test this yourself by running a short segment with and without the restraint and then taking a look

[gmx-users] lipidposre.itp file of popc

Hi gmx-archives, I want do *PR for popc with restrain specifically on P(8),C(50),CA1(50) of all popc molecules, I wrote lipidposre.itp file like this [ position_restraints ] ; atom type fx fy fz 8 1 500 500 500 501 500 500 500 511 500 500

[gmx-users] Leaflet of Bilayer

In my opinion, use any technique that you want (genbox included) then run the resulting system for >=50ns while plotting the area per lipid and order parameters over time. When these values stop drifting over time then you have an equilibrated bilayer. If you have access to a cluster that s

[gmx-users] Multiple ppa files from a single parallel mdrun_mpi job

After taking a closer look at the code, I suspect that the problem can be resolved as follows. The call to: read_pullparams(pull, opt2fn("-pi",nfile,fnm), opt2fn("-po",nfile,fnm)); in pullinit.c should probably be protected by: if (MASTER(cr)) I have not tested this as it doesn't really matter

[gmx-users] TIP4P and TIP5P

Hi Could anyone tell me how to construct the solvent box of TIP4P and TIP5P model? And, how to construct water_TIP4P.itp and and water_TIP5P.itp ? Thank you very much Lin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailm

[gmx-users] how many water molecule used to run MD?

Hi how many water molecules used to run MD? what is the criteria for this? I found some water.gro including 216 or 512 water molecules. Is it enough to include 216 or 512 water molecules only in MD system? For TIP4P; there are 4 coordinates to determine a water molecule. For TIP5P; there are

[gmx-users] Cann't get the same result ?

Hi all: I run mdrun of gromacs-3.3.3 6 times of a small simulation, but I cann't get the same result every time. I run the mdrun program using "./mdrun -v -s md1.tpr -o md1.trr -c after_md1.gro -g md1.log -e md1.edr -x md1.xtc > md1.job && ./mdrun -v -s md1.tpr -o md1.trr -c after_md

[gmx-users] How to implement v-rescale thermostat in gromacs-3.3.3

Hi gmx-users, When I came across the 4.0 beta version, I found there was a new thermostat named v-rescale available here. I wonder if it would be easy to incorporate it in the version 3.3.3 as a patch. Note that the 4.0 version is still under development, I prefer to use a revised 3.3.3 version

Re: Re: [gmx-users] Re: Leaflet of Bilayer

Thanks for the response Just diverting this topic to about specific number of popc molecules. I created the bilayer by using genconf command genconf -f popc128a.pdb -o out.gro -dist 0 0 0 -nbox 2 1 1 (as I posted in my previous mail) generated output file contain 128 popc in each leaflet of

[gmx-users] Re: gmx-users Digest, Vol 53, Issue 90

Hi Ran Thank you for your reply. I'm sorry that I miss the message. >(1) 6 eigenvalues represent rotation and translation. For (very) small >molecules, these can be quite substantial, see Carlsson and Aqvist, /J. >Phys. Chem. B,/ *109* (13), 6448 -6456, 2005. By fitting you remove the >rotation a

[gmx-users] PME 3dc geometry and the optimal PME mesh load

Hi all, I use 3dc geometry for a system with large box size in z direction, and when I try the new CVS version, I find a note saying "The optimal PME mesh load is usually between 025 and 0.33, you should probably increase the cut-off and the PME grid spacing". A quite large estimation 0.86 was rep

[gmx-users] RE: DMSO-protein simulation

> how to calculate c6 & c12 coloumn for DMSO > thanx in advance Search for C6 and C12 for DMSO or for sigma and epsilon in the literature. -- Vitaly V. Chaban School of Chemistry National University of Kharkiv Svoboda sq.,4, Kharkiv 61077, Ukraine email: [EMAIL PROTECTED] skype: vvchaban tel.:

[gmx-users] RE: Gromacs 4.0 beta1

> What is the link to download binaries and source code for Gromacs 4.0 beta1? Type in google "gromacs CVS" -- Vitaly V. Chaban School of Chemistry National University of Kharkiv Svoboda sq.,4, Kharkiv 61077, Ukraine email: [EMAIL PROTECTED] skype: vvchaban tel.: +38-097-8259698 __