Re: [gmx-users] Umbrella sampling

I attached md_pull.mdp file i put " cutoff-scheme = group" beecause of some errors (about energy groups) This is what i try to do(part of some literatures); 1-pulling the CM of the object along the z-axis—perpendicular to the surface of ZnO 2-Pulling is implemented through a “dummy particle”

Re: [gmx-users] Umbrella sampling

On 11/24/17 9:14 AM, Rose wrote: Hello I'm beginner in GROMACS. I'm using umbrella sampling(helping from its tutorial with MR Lemkul) But I don't know how should I implement deltaZ and how choose different conf.gro and which will be useful for further sampling. To tell the truth I couldn't

Re: [gmx-users] Problem to compute interaction energy between different groups

On 11/24/17 11:00 AM, ARNAB MUKHERJEE wrote: Hello, I have simulated a system of DNA and Protamine (Coarse grained, Martini). I want to look at the interaction energy between different groups like DNA - Protamine, DNA - ions, etc. I have defined energy groups in the mdp file, and I pass the

[gmx-users] Problem to compute interaction energy between different groups

Hello, I have simulated a system of DNA and Protamine (Coarse grained, Martini). I want to look at the interaction energy between different groups like DNA - Protamine, DNA - ions, etc. I have defined energy groups in the mdp file, and I pass the index file with the groups while building the tpr

[gmx-users] Umbrella sampling

Hello I'm beginner in GROMACS. I'm using umbrella sampling(helping from its tutorial with MR Lemkul) But I don't know how should I implement deltaZ and how choose different conf.gro and which will be useful for further sampling. To tell the truth I couldn't get summary.dat by "perl distance.pl"

Re: [gmx-users] Does RMSD only consider the "relative" coordinate changes for the selected group?

Dear Justin and Peter, Thank you so much! I did not realise the meaning of two prompts until now. I was always using the same number for the two prompts. Thank you for the MDAnalysis! https://www.mdanalysis.org/pages/learning_MDAnalysis/ Yours sincerely Cheng --

Re: [gmx-users] Does RMSD only consider the "relative" coordinate changes for the selected group?

On 24-11-17 13:48, Justin Lemkul wrote: > > > On 11/24/17 5:25 AM, ZHANG Cheng wrote: >> Dear Justin, >> Thank you for confirming this. May I ask, >> >> >> 1) How to "fit to the whole protein (or backbone, CA, etc) and >> subsequently calculate the RMSD of given residue(s)"? >> >> >> My current

Re: [gmx-users] Does RMSD only consider the "relative" coordinate changes for the selected group?

On 11/24/17 5:25 AM, ZHANG Cheng wrote: Dear Justin, Thank you for confirming this. May I ask, 1) How to "fit to the whole protein (or backbone, CA, etc) and subsequently calculate the RMSD of given residue(s)"? My current command is (by selecting the residue in the "index.ndx" file): gmx

Re: [gmx-users] Does RMSD only consider the "relative" coordinate changes for the selected group?

Dear Justin, Thank you for confirming this. May I ask, 1) How to "fit to the whole protein (or backbone, CA, etc) and subsequently calculate the RMSD of given residue(s)"? My current command is (by selecting the residue in the "index.ndx" file): gmx rms -s md_0_1.tpr -f md_0_1_noPBC.xtc -n

Re: [gmx-users] virtual site connected to dummy massive site

Hi, Potential energy is a function of configuration. You can expect the same LJ energy if you compare the same configuration, ie that the distribution of states is identical. But if you would have the same total energy and a different distribution between PE and KE (because the DOF change) then

Re: [gmx-users] Regarding calculating the water orientation profile

Hi, Why do you want to do something when you don't understand what it is or whether it will be useful? Mark On Fri, Nov 24, 2017 at 9:08 AM Dilip H N wrote: > So what exactly does this Orientation Profile means.?? > I am really confused with the exact approach

Re: [gmx-users] virtual site connected to dummy massive site

Dear Mark, thanks, but degrees of freedom goes to kinetic energies, still LJ energies must be the same, yes? Best regards On Fri, Nov 24, 2017 at 8:22 AM, Mark Abraham wrote: > Hi, > > Your systems have different available degrees of freedom, so they sample >

Re: [gmx-users] Regarding calculating the water orientation profile

Orientation has nothing to do with proximity. You can have orientation as a function of proximity, but orientation *per se* does not necessarily involve a distance, it just tells you about a preferential orientation of the water molecules towards a reference. We've already been through this in

Re: [gmx-users] Topology file of molecule

Dear Magnus and Justin, Thank you very much for your help. Kind regards, Krzysztof 2017-11-23 13:55 GMT+01:00 Justin Lemkul : > > > On 11/23/17 7:51 AM, Magnus Lundborg wrote: > >> Dear Krzysztof, >> >> I wouldn't be too worried about the fact that GAFF parameters have been >>

Re: [gmx-users] Regarding calculating the water orientation profile

So what exactly does this Orientation Profile means.?? I am really confused with the exact approach towards it... Sent with Mailtrack