Re: [gmx-users] question about g_density

Hi! Follow up question on this. I'm getting the xvg file i want but the interval is .5. This is too big for me since I want to get the bilayer thickness. what additional options should I add to g_density -f confout.gro -n index.ndx -o martini.xvg to get a better xvg output file. BTW, I

Re: [gmx-users] g_rms -dist option

On 2/14/14, 5:58 AM, Kavyashree M wrote: Dear users, The option -dist in g_rms is not clear from the manual. Does it give the rmsd distribution? if not how to get an rmsd distribution (other than writing a code). It is there in g_cluster but I am not able to understand the plot it gives for

Re: [gmx-users] g_rms -dist option

Ok. Thank you. Regards Kavya On Fri, Feb 14, 2014 at 5:44 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/14/14, 5:58 AM, Kavyashree M wrote: Dear users, The option -dist in g_rms is not clear from the manual. Does it give the rmsd distribution? if not how to get an rmsd distribution

[gmx-users] Simulations in extreme conditions

Hi everyone! I am trying to run a simulation of methane-water mixtures under extreme conditions, that is around 25 kbars and 600K (and maybe higher in both pressure and temperature). I am currently using OPLS for methane with TIP3P for water. The way I proceed is as follows: -generate a box of

Re: [gmx-users] Simulations in extreme conditions

On 2/14/14, 1:58 PM, CipPruteanu wrote: Hi everyone! I am trying to run a simulation of methane-water mixtures under extreme conditions, that is around 25 kbars and 600K (and maybe higher in both pressure and temperature). I am currently using OPLS for methane with TIP3P for water. The way I

[gmx-users] Warning: atom is missing in residue

Hi gmx users, When I run gromacs, there is an issue with the molecules with more than one residue. for example, for this pdb file: ATOM 1 C1 VOD 0 8.441 1.158 0.141 1.00 0.00 C ATOM 2 H1 VOD 0 9.420 1.340 0.570 1.00 0.00 H

Re: [gmx-users] Warning: atom is missing in residue

On 2/14/14, 6:24 PM, Ehsan Sadeghi wrote: Hi gmx users, When I run gromacs, there is an issue with the molecules with more than one residue. for example, for this pdb file: ATOM 1 C1 VOD 0 8.441 1.158 0.141 1.00 0.00 C ATOM 2 H1 VOD 0 9.420

Re: [gmx-users] order parameter

I cannot locate the VMD script to calculate the tetrahedral order parameter. Does anyone know where I can find it? Alternatively, the manual states that g_order can compute this parameter, but it is not clear to me how to do so. It seems like this command is tailored for carbon tails. I would

Re: [gmx-users] Warning: atom is missing in residue

Thanks Justin. But I found some residue int the rtp file which have more than one residue inside them such as: [ TYR ] [ atoms ] N N-0.31000 0 H H 0.31000 0 CA CH1 0.0 1 CB CH2 0.0 1 CG C 0.0 1 CD1 C

Re: [gmx-users] Warning: atom is missing in residue

On 2/14/14, 7:30 PM, ehs wrote: Thanks Justin. But I found some residue int the rtp file which have more than one residue inside them such as: [ TYR ] [ atoms ] N N-0.31000 0 H H 0.31000 0 CA CH1 0.0 1 CB CH2 0.0 1 CG

Re: [gmx-users] order parameter

On 2/14/14, 7:55 PM, rankinb wrote: Is g_hydorder available only in certain versions of GROMACS? I am using version 4.5.3 and it says that g_hydorder is not found. Perhaps it is time to update. I think it used to be called g_h2order, but yes, 4.5.3 is rather ancient. -Justin --

[gmx-users] charges in vaccum simulations

Hello all I have a small query regarding neutralization of charges in vaccum simulations. I would like to simulate in vaccum 10 copies of 10 residue peptide containing one charged residue lysine (I am interested in monitoring cation-pi interactions between them). 1) Would you suggest me to