Re: [gmx-users] V(R) around protein

from the surface of the protein. Nihal On Mon, Sep 12, 2011 at 6:42 PM, E. Nihal Korkmaz wrote: > R is any distance from the surface of the protein. > > > On Mon, Sep 12, 2011 at 6:31 PM, Mark Abraham wrote: > >> On 13/09/2011 9:29 AM, E. Nihal Korkmaz wrote: >> &g

Re: [gmx-users] V(R) around protein

R is any distance from the surface of the protein. On Mon, Sep 12, 2011 at 6:31 PM, Mark Abraham wrote: > On 13/09/2011 9:29 AM, E. Nihal Korkmaz wrote: > >> Dear all, >> >> Is there any function to get the Volume around a peptide/protein as a >> function of R?

[gmx-users] V(R) around protein

Dear all, Is there any function to get the Volume around a peptide/protein as a function of R? The problem is g_rdf -surf doesn't have a volume correction factor, so my aim is to apply a volume correction factor manually by having V(R) around the protein. Thanks, -- Elif Nihal Korkmaz Researc

[gmx-users] g_covar -xmpa

Dear all, Is there a "trick" to get the numbers for g_covar -xmpa? If not how can i calculate -xmpa results from -xpm -ascii results? Thanks Nihal -- Elif Nihal Korkmaz Research Assistant University of Wisconsin - Biophysics Member of Qiang Cui & Thomas Record Labs 1101 University Ave, Rm. 835

Re: [gmx-users] SPC/E water for Charmm ff implementation

s spc/e parameters for c27, i want to play with the parameters that's why i am asking the file read. Thanks, Nihal On Wed, Jul 20, 2011 at 11:05 PM, Mark Abraham wrote: > On 21/07/2011 12:59 PM, E. Nihal Korkmaz wrote: > >> Dear all, >> >> I was trying to see th

[gmx-users] SPC/E water for Charmm ff implementation

Dear all, I was trying to see the LJ parameters for SPC/E water in Charmm27.ff implementation in Gromacs. In the ffnonbonded.itp file i can see parameters for TIP3P, TIP4P, SPC but not for SPC/E. Does SPC/E use the same parameters with SPC? (but the charges listed in the ffnonbonded.itp is differe

[gmx-users] protein simulation w/ urea + water

Dear all, I am trying to simulate a protein in urea solution. I used *genbox -cp protein_in_box.gro -cs urea+h2o.gro -o out.gro -p topology* but the resulting topology doesn't contain any information on urea nor the atoms of urea. I also tried adding ureas on the protein with *-ci urea_single.gro

[gmx-users] dodecahedron, octahedron box

Dear all, I am trying to solvate a protein in a dodecahedron box, and the box doesn't seem right. I tried *trjconv -s ur compact -pbc mol, *that ended up with a dodecahedron shaped water distrubution around the protein however the box is still shown as triclinic inbn Pymol? Is this Pymol's weakne

[gmx-users] implicit solvent system set up

Dear all, This may sound stupid, but just to make sure that I am right track about implicit solvent simulations, the set up involves pdb2gmx editconf grompp I mean, we still need to define the box dimensions by editconf and apply periodicity, right? Besides, what type of ensemble would be a good

Re: [gmx-users] Re: LINCS WARNING relative constraint deviation

What would you suggest as a short time step? I was using 0.002 ps. And just to make sure, would 5 ns of equilibration be enough for a ~110 amino acid long protein? Thanks, Nihal On Mon, Jun 20, 2011 at 7:41 AM, Mark Abraham wrote: > ** > On 20/06/2011 3:29 PM, E. Nihal Korkmaz wrote: >

[gmx-users] Re: LINCS WARNING relative constraint deviation

I assume the structure is not relaxed enough to start a simulation. How can I get it minimize further? I increased the step size up to 0.1 ps, i still get the same result. Thanks, Nihal On Sun, Jun 19, 2011 at 11:48 PM, E. Nihal Korkmaz wrote: > Dear all, > > I am trying to simulate a GB s

[gmx-users] LINCS WARNING relative constraint deviation

Dear all, I am trying to simulate a GB simulation of a 112 amino acid long protein. I keep getting these errors, Step 27718, time 55.436 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 33.319842, max 438.763717 (between atoms 79 and 81) bonds that rotated more than 30 degrees:

Re: [gmx-users] load imbalance

Thanks for the reply. Would that cause any problems in the simulation? It says force 154.9%, does that mean it is applying the wrong force? Is it safe to proceed to simulation like that? Thanks, Nihal On Thu, Jun 16, 2011 at 9:54 PM, Mark Abraham wrote: > ** > On 17/06/2011 12:44 PM, E.

[gmx-users] cross correlations

Dear all, Is there any built in function that gives me the pairwise correlation of the fluctuation (unit vector between two coordinates of a residue) of residues (averaged over the input trajectory). I tried g_covar but that's not what i'm looking for. The result I want should be an NxN matrix wit

[gmx-users] load imbalance

Hi all, I am trying to run GB model simulation of a small protein. I keep getting these errors for every step printed to the log file. DD load balancing is limited by minimum cell size in dimension X DD step 35999 vol min/aver 0.799! load imb.: force 154.9% Below i copied my mdp parameters. I