[gmx-users] Re: hydrophobic contacts

Hi all thanks for your valuable suggestions. But still i'm not clear. I have tried using the .tpr file with make_ndx but the index group is displayed is similar to that of the one with .gro file. I have manually identified the residues and when i ran the g_mindist with the ligand 0f 18 atoms again

Re: [gmx-users] Gromacs 4.6 segmentation fault with mdrun

Hi Raf, which version of Gromacs did you use? If you used branch nbnxn_hybrid_acc please use branch release-4-6 instead and see whether that fixes your issue. If not please open a bug and upload your log file and your tpr. Roland On Thu, Nov 15, 2012 at 5:13 PM, Raf Ponsaerts < raf.ponsae...@me

Re: [gmx-users] NMA proctocol

On 11/16/12 6:44 PM, Yao Yao wrote: Hi Gmxers, For Normal Mode Analysis (NMA), even I did run several rounds to aim for machine precision, with smaller emtol stepwise, it still did not converge to 0.001 and the Fmax is about 0.5 or so. It is just lysozyme in 200 water molecules. Are you

[gmx-users] NMA proctocol

Hi Gmxers, For Normal Mode Analysis (NMA), even I did run several rounds to aim for machine precision, with smaller emtol stepwise, it still did not converge to 0.001 and the Fmax is about 0.5 or so. It is just lysozyme in 200 water molecules. I wonder if there is a systematic way to guarantee

Re: [gmx-users] Dihedral form

And get the use of radians right! Mark On Nov 15, 2012 4:01 PM, "Erik Marklund" wrote: > Hi, > > 15 nov 2012 kl. 15.41 skrev Laura Leay: > > > Thanks Eric, > > > > Just to clarify (I hope this notation is in fact clear): > > > > E=0.5k [ 1 - cos( n*phi - n*phi_o +180 ) ] = 0.5k [ 1 + cos(n*phi

Re: [gmx-users] partial charges and radius setting

On 11/16/12 3:12 AM, Rajiv Gandhi wrote: Dear Gmx users, I want to know how to set the particular value of effective partial charges CO ligand in topology file ? For non bonded interaction(12-6 Lennard-Jones potential function) how do i set a radius and well depth parameter for CO ? Parame

Re: [gmx-users] Fe(2+) nonbonded parameters

On 11/16/12 4:01 AM, Steven Neumann wrote: On Thu, Nov 15, 2012 at 5:51 PM, Justin Lemkul wrote: On 11/15/12 12:47 PM, Steven Neumann wrote: So what would you do to get those parameters asap? Get what parameters? The ones shown below (except Cu2+) have no citation and no one has vouch

Re: [gmx-users] Force vs distance plot in pulling simulation?

On 11/16/12 10:45 AM, Gmx QA wrote: Hello gmx-users, I've performed a pulling simulation and obtained a force-vs-time plot and a distance-vs-time plot (xvg-files). Is it common to somehow combine these to get a force-vs-distance-plot using a hacked-together script, or how do people that have e

Re: [gmx-users] NMA Fatal Error

On 11/16/12 3:43 PM, Yao Yao wrote: Hi Gmxers, I am doing a protein NMA with the mdp file like, === define = -DEFLEXIBLE constraints = none integrator = nm ; emtol = 0.1 emstep = 0.1 nsteps = 4000 ; M

[gmx-users] NMA Fatal Error

Hi Gmxers, I am doing a protein NMA with the mdp file like, === define  = -DEFLEXIBLE constraints = none integrator  = nm ; emtol   = 0.1 emstep  = 0.1 nsteps  = 4000  ; Maximum number of (minimization) steps to

Re: [gmx-users] problem in running md simulation

Oh, I am sorry That is right. But its difficult to find The specific cutoff values to be used for different protocols of cutoff, switch and shift.. different values are stated in different papers.. And original force field paper (eg OPLSAA) does not explicitly specify these values. Any references r

Re: [gmx-users] Re: Umbrella sampling question

Thanks Erik! /PK 2012/11/16 Erik Marklund > Hi, > > Blindly defining the center of mass for a group of atoms is not possible > in a periodic system such as a typical simulation box. You need some clue > as to which periodic copy of every atom that is to be chosen. By providing > pull_pbcatom0 y

Re: [gmx-users] GPU warnings

Hi Albert, Apologies for hijacking your thread. Do you happen to have Fedora 17 as well? -- Szilárd On Sun, Nov 4, 2012 at 10:55 AM, Albert wrote: > hello: > > I am running Gromacs 4.6 GPU on a workstation with two GTX 660 Ti (2 x > 1344 CUDA cores), and I got the following warnings: > > tha

Re: [gmx-users] GPU warnings

Hi Thomas, The output you get means that you don't have any of the macros we try to use although your man pages seem to be referring to them. Hence, I'm really clueless why is this happening. Could you please file a bug report on redmine.gromacs.org and add both the initial output as well as my pa

Re: [gmx-users] problem in running md simulation

On 11/16/12 10:10 AM, Kavyashree M wrote: Hi Ananya, Can you try with rvwd 0.9nm and rcolumb with 1.4nm..? vdw interaction decreases as 1/r^6, while columbic interaction decreases as (1/r).. so it would be better if you consider columbic interaction for longer distance than vdw interaction..

Re: [gmx-users] problem in running md simulation

Hi Ananya, Can you try with rvwd 0.9nm and rcolumb with 1.4nm..? vdw interaction decreases as 1/r^6, while columbic interaction decreases as (1/r).. so it would be better if you consider columbic interaction for longer distance than vdw interaction.. bye kavya On Fri, Nov 16, 2012 at 8:32 PM, an

Re: [gmx-users] problem in running md simulation

Hi all, As suggested by venhat I have energy minimised it till 1000Kj/mol but even now I am getting the same error, saying Warning: 1-4 interaction between 3230 and 3233 at distance 3.573 which is larger than the 1-4 table size 2.400 nm These are ignored for the rest of the simulation This u

[gmx-users] Bug (?) with FEP while using particle decomposition in charge transformation

Dear all, I have faced a very strange results while using the FEP together with particle decomposition in charge transformation. Situation is as follows: gromacs-4.5.5, single precision, mpi-run on 32 nodes; only charges are modified in the topology file (VdW and massess remains the same for A

Re: [gmx-users] Re: Umbrella sampling question

Hi, Blindly defining the center of mass for a group of atoms is not possible in a periodic system such as a typical simulation box. You need some clue as to which periodic copy of every atom that is to be chosen. By providing pull_pbcatom0 you tell gromacs to, for every atom in grp0, use the pe

Re: [gmx-users] Fe(2+) nonbonded parameters

On Thu, Nov 15, 2012 at 5:51 PM, Justin Lemkul wrote: > > > On 11/15/12 12:47 PM, Steven Neumann wrote: >> >> So what would you do to get those parameters asap? >> > > Get what parameters? The ones shown below (except Cu2+) have no citation > and no one has vouched for their authenticity. As suc

[gmx-users] Re: g(r) does not go to 1 at long r -- bug in g_rdf?

Thanks David, I filed bug #1036. Regards, Pablo -- View this message in context: http://gromacs.5086.n6.nabble.com/g-r-does-not-go-to-1-at-long-r-bug-in-g-rdf-tp5003015p5003018.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@g

Re: [gmx-users] Strange form of RDF curve

On 2012-11-15 18:53, shch406 wrote: Dear Gromacs users, I tried g_rdf function and have obtained a strange result: usually the RDF curve looks like relaxing oscillations around 1.0 constant level, but in my case it appears to be oscillation around exponent going from 0.0 at zero distance to 1.0

Re: [gmx-users] g(r) does not go to 1 at long r -- bug in g_rdf?

On 2012-11-16 09:12, Pablo Englebienne wrote: Hi, I tried to calculate the radial distribution functions for a simple system: a 5nm a side cubic box with 10 Ne atoms and 10 Ar atoms, simulated for 100ns in NVT @ 300K. I was expecting to get an RDF with a peak, stabilizing to 1.0 at long distance

[gmx-users] g(r) does not go to 1 at long r -- bug in g_rdf?

Hi, I tried to calculate the radial distribution functions for a simple system: a 5nm a side cubic box with 10 Ne atoms and 10 Ar atoms, simulated for 100ns in NVT @ 300K. I was expecting to get an RDF with a peak, stabilizing to 1.0 at long distances. This was the case for the Ne-Ar RDF, but