[gmx-users] what restraint can I use to prevent membrane diffusion along the Z-axis?

Dear GROMACS users, While simulating a DLPC membrane, I noticed that it tends to diffuse along the normal (Z-axis) component. Is there a 'standard' restrain that is used to prevent such diffusion? The first option I thought was to restrain the center of mass of the whole membrane along the Z-axis

Re: [gmx-users] what restraint can I use to prevent membrane diffusion along the Z-axis?

9:04 PM, Mark Abraham wrote: > On 23/02/2012 10:26 AM, Jose Borreguero wrote: > > Dear GROMACS users, > > While simulating a DLPC membrane, I noticed that it tends to diffuse along > the normal (Z-axis) component. Is there a 'standard' restrain that is used > to prev

Re: [gmx-users] what restraint can I use to prevent membrane diffusion along the Z-axis?

remove the COM momentum in this case? -Jose On Thu, Feb 23, 2012 at 8:35 AM, Mark Abraham wrote: > On 23/02/2012 10:27 PM, Jose Borreguero wrote: > > I am not referring to any drift of the whole system, but to the diffusion > of the lipid bilayer only. Diffusion of molecules in wa

[gmx-users] how to obtain NOEs from MD trajectory ?

Dear Gromacs users, Is there any algorithm/procedure to calculate NOEs from an MD trajectory? I'd greatly appreciate any references where the algorithm is described. Best regards, Jose M. Borreguero -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-

[gmx-users] Newbie: Which implicit solvent force field to choose?

Dear Gromacs users, I'm new to gromacs. I want to simulate a short peptide in an implicit solvent with low dielectric constant (simulate the interior of a membrane). Can you please tell me which implicit solvent force field is more suitable, and how do I pass the value of the dielectric constant ?

[gmx-users] Newbie: How to modify the topology file after adding ions?

Dear Gromacs users, Im new to gromacs and I'm following a tutorial ( http://nmr.chem.uu.nl/~tsjerk/course/molmod/). Unfortunately, the tutorials doesn't say anything about how to update the topology file after using 'genion' to replace a few water molecules with ions. I manually edited the topolog

Re: [gmx-users] Newbie: How to modify the topology file after adding ions?

ne 7228 of protein.top is the last line of the file, that is, CL 23 So the error message is not much help :( -Jose On Wed, Dec 7, 2011 at 11:04 AM, Justin A. Lemkul wrote: > > > Jose Borreguero wrote: > >> Dear Gromacs users, >> >> Im new to gromacs and I'

Re: [gmx-users] Newbie: How to modify the topology file after adding ions?

ls :D ( http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html) I'll give a try with the Lyzosyme one! - Jose On Wed, Dec 7, 2011 at 1:29 PM, Justin A. Lemkul wrote: > > > Jose Borreguero wrote: > >> Hi Justin, thanks for your reply! >> >> I appended

Re: [gmx-users] Newbie: How to modify the topology file after adding ions?

gt; paragraph was not edited or added. > > Although I feel personally addressed, I can add that you're not the > first to respond to the tutorial like this. It is common behaviour for > a subset of undergrad students that had to follow this course as part > of their curriculum

[gmx-users] isopropanol parameters?

Dear GROMACS users, I am simulating aqueous isopropanol. Unfortunately I observe segregation of isopropanol from SPC water at isopropanol fraction volume of 0.25. Since isopropanol is miscible in water, my parameters stress too much the hydrophobic character of this solute. Only a few interstitial

Re: [gmx-users] isopropanol parameters?

0.106023 "HA2" 0.038591 "HA3" 0.038591 "O1"-0.579340 "HO1" 0.373996 And the VdW radii and epsilon: HC 1.3770 0.0150 OH 1.7210 0.2104 CT 1.9080 0.1094 HO 0.0 0.0 On Fri, Mar 5, 2010 a