Re: [gmx-users] rmsf question

Dear Mark and Tjerk, Thank you for your comments. If I correctly uderstand the RMSF computed on C-alpha in PDB NMR structure, is a measure of the uncertanty in resolving the structure. Compared to this the RMSF of C-alpha computed from a MD trajectory reflects the geometric fluctuations of the bac

[gmx-users] oxydiffusion

Respected experts Thank you a lot for your valuable suggestions for my previous mail.   Taking your advice I used SPCE water model with ffg43a1 forcefield. I modified the non bonded parameters for oxygen-water interaction taking the parameters from CRC as a source in the nonbonded parameter file.

[gmx-users] oxydiff

In the previous mail I forgot to attach the msd curve. Would you please give a glance at this graph in relation to my previous mail ??    Thank you for your consideration Neal <>-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please s

Re: [gmx-users] rmsf question

On Mar 16, 2010, at 9:43 AM, Andrei Neamtu wrote: Dear Mark and Tjerk, Thank you for your comments. If I correctly uderstand the RMSF computed on C-alpha in PDB NMR structure, is a measure of the uncertanty in resolving the structure. Well, the "uncertainty of the NMR experiment" would be stro

Re: [gmx-users] rmsf question

On 16/03/2010 8:17 PM, XAvier Periole wrote: On Mar 16, 2010, at 9:43 AM, Andrei Neamtu wrote: Dear Mark and Tjerk, Thank you for your comments. If I correctly uderstand the RMSF computed on C-alpha in PDB NMR structure, is a measure of the uncertanty in resolving the structure. Well, the "u

Re: [gmx-users] rmsf question

On Mar 16, 2010, at 10:24 AM, Mark Abraham wrote: On 16/03/2010 8:17 PM, XAvier Periole wrote: On Mar 16, 2010, at 9:43 AM, Andrei Neamtu wrote: Dear Mark and Tjerk, Thank you for your comments. If I correctly uderstand the RMSF computed on C-alpha in PDB NMR structure, is a measure of the

Re: [gmx-users] rmsf question

Hi Andrei, > If I correctly uderstand the RMSF computed on C-alpha in PDB NMR > structure, is a measure of the uncertanty in resolving the structure. No, that's not what I said. You're saying that there's one structure (the structure), but there is uncertainty in resolving it. That's not the case

Re: [gmx-users] cross-correlations as a function of interatomic distance

Hi, Well, since interatomic distances are properties of single conformations and fluctuation covariances/correlations are properties of sets of conformations, it is simply impossible. You might plot the covariances/correlations against the mean distances, if you feel you must. Be sure to use the a

[gmx-users] Thickness

Hi, I used bilayer that consisted of 128 DOPC lipids as DOPC128.pdb as the primary bilayer and insert protein in bilayer with Inflategro program. when i expanded the bilayer, two DOPC molecules exited from box. i simulated this system and obtained the thickness of bilayer with GrigMAT_MD. i wan

Re: [gmx-users] Thickness

afsaneh maleki wrote: Hi, I used bilayer that consisted of 128 DOPC lipids as DOPC128.pdb as the primary bilayer and insert protein in bilayer with Inflategro program. when i expanded the bilayer, two DOPC molecules exited from box. i simulated this system and obtained the thickness of b

[gmx-users] g_rdf

Dear gromacs users, I want to calculate radial distribution function around my protein. I want to get g_rdf for water molecules (OW) around my protein and g_rdf for COM of some solutes around my protein. The numbers should be averaged over all the frames. I tried to look at the mailing list

Re: [gmx-users] g_rdf

pol...@fh.huji.ac.il wrote: Dear gromacs users, I want to calculate radial distribution function around my protein. I want to get g_rdf for water molecules (OW) around my protein and g_rdf for COM of some solutes around my protein. The numbers should be averaged over all the frames. I tried

[gmx-users] implicit solvent

Does anyone know how to implement implicit solvent in the Concurrent version system ? Thanks -- Milad Ekramnia Physics Department Isfahan University of Technology -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive a

Re: [gmx-users] g_rdf

pol...@huji.ac.il wrote: While trying to search throw mailing list I'm getting the next error "/content/body/p[2]/span, function 'RecordList' failed " The site is intermittently buggy, although it seems to be working fine now. I'm not interested in basic information. I'm using "g_rdf -f

[gmx-users] FEP dEkin/dlambda dG/dl constr. values continuously coming out 0.00000e+00

Hello All, My earlier error ie. dVpot/dlambda values coming zero is solved now But still two values dEkin/dlambda dG/dl constr as continously coming zero. I understand that for free energy calculation only dVpot/dlambda are required. So, should I ignore these two values and proceed with the

Re: [gmx-users] mix berger ff with opls

Dear Chris: Now it makes all sense. Thanks a lot. And your method surly works great. Bin On Mar 15, 2010, at 9:23 AM, chris.ne...@utoronto.ca wrote: Dear Bin, I think that you are getting confused here between different publications. It was the Lindahl, E., and O. Edholm. 2000. paper tha

Re: [gmx-users] FEP dEkin/dlambda dG/dl constr. values continuously coming out 0.00000e+00

Those derivatives should be zero: the kinetic energy is determined by your thermostat and shouldn't change as a function of lambda - as it should for any normal free energy calculation in constant-temperature ensembles. Also, the constraint energy doesn't change as lambda changes (only the van de

[gmx-users] Gromacs website

It looks like the Gromacs site is having some difficulties. Several recent updates to the wiki pages have reverted (anything in the past week or so is gone), the site search does not work, and when comparing page revisions, no content is displayed. There may be other problems, but those are

[gmx-users] g_wham error

Here's my .xvg: # This file was created Mon Mar 8 01:50:07 2010 # by the following command: # /opt/apps/intel10_1/mvapich1_1_0_1/gromacs/4.0.5/bin/mdrun_mpi -multi 31 -deffnm onePREP -px onePREP -np 2976 -maxh 3 # # /opt/apps/intel10_1/mvapich1_1_0_1/gromacs/4.0.5/bin/mdrun_mpi is part of G R O M

Re: [gmx-users] g_wham error

Gard Nelson wrote: Here's my .xvg: # This file was created Mon Mar 8 01:50:07 2010 # by the following command: # /opt/apps/intel10_1/mvapich1_1_0_1/gromacs/4.0.5/bin/mdrun_mpi -multi 31 -deffnm onePREP -px onePREP -np 2976 -maxh 3 # # /opt/apps/intel10_1/mvapich1_1_0_1/gromacs/4.0.5/bin/mdr

Re: [gmx-users] g_wham error

Justin A. Lemkul wrote: Gard Nelson wrote: Here's my .xvg: # This file was created Mon Mar 8 01:50:07 2010 # by the following command: # /opt/apps/intel10_1/mvapich1_1_0_1/gromacs/4.0.5/bin/mdrun_mpi -multi 31 -deffnm onePREP -px onePREP -np 2976 -maxh 3 Note, too, that this command doe

[gmx-users] density vs time

Hello, I am simulating one methane molecule in 899 water molecues in the box size of 3 3 3 nm (27nm^3). I would like to determine density vs time. Is there a way I can do that? I am running my simulation at constant Volume i.e. no pressure coupling. I tried using g_density but it give

Re: [gmx-users] density vs time

nishap.pa...@utoronto.ca wrote: Hello, I am simulating one methane molecule in 899 water molecues in the box size of 3 3 3 nm (27nm^3). I would like to determine density vs time. Is there a way I can do that? I am running my simulation at constant Volume i.e. no pressure coupling. I tri

Re: [gmx-users] density vs time

Justin A. Lemkul wrote: nishap.pa...@utoronto.ca wrote: Hello, I am simulating one methane molecule in 899 water molecues in the box size of 3 3 3 nm (27nm^3). I would like to determine density vs time. Is there a way I can do that? I am running my simulation at constant Volume i.e.

RE: [gmx-users] density vs time

g_energy Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hamm

Re: [gmx-users] density vs time

I am trying to get an rdf graph actually, and my values are very close to one, but not exactly one, and I was wondering if there is some normalization issue with g_rdf? These are my values for rdf: 0 0 0.002 0 0.004 0 0.006 0 0.008

Re: [gmx-users] density vs time

nishap.pa...@utoronto.ca wrote: Near the end, the values are fluctuating around one. The reason I was That would seem right to me. trying to get density values was may be to try an understand if the density computed by gromacs is different for just water system and water+one methane sys

[gmx-users] implcit solvent

Does anyone know how to implement implicit solvent for proteins in the concurrent version system (CVS) of Gromacs? -- Milad Ekramnia Physics Department Isfahan University of Technology -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please

[gmx-users] Re: density vs time

> > I am trying to get an rdf graph actually, and my values are very close > to one, but not exactly one, and I was wondering if there is some > normalization issue with g_rdf? These are my values for rdf: > >   0          0 >      0.002          0 >      0.004          0 >      0.006          0 >

[gmx-users] gromacs 4.0 on CRAY-XT4

Dear all: I was trying to build gromacs 4.0 on a cray-xt4 machine, the same one as the benchmark in the gromacs4 paper (). However, my timing for a similar system, ~100,000 atoms, is almost 3 times slower than in the paper. For example, I only got ~25 ns/day with 128 cpus. So is there any