[gmx-users] Fwd: REgarding for the disulphide bond

-- Forwarded message -- From: Sathish Kumar sathishk...@gmail.com Date: Sun, Jan 27, 2013 at 2:02 PM Subject: REgarding for the disulphide bond To: gmx-users@gromacs.org Sir, I am sathish kumar working as junior research fellow.I have taken pdb file from protein data

[gmx-users] Re: gromacs 4.6 GB/SA problem and poor performance

Using ICC 13.0, I got a same result. -- View this message in context: http://gromacs.5086.n6.nabble.com/gromacs-4-6-GB-SA-problem-and-poor-performance-tp5004729p5004922.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list

Re: [gmx-users] Fwd: REgarding for the disulphide bond

On 1/27/13 3:39 AM, Sathish Kumar wrote: -- Forwarded message -- From: Sathish Kumar sathishk...@gmail.com Date: Sun, Jan 27, 2013 at 2:02 PM Subject: REgarding for the disulphide bond To: gmx-users@gromacs.org Sir, I am sathish kumar working as junior research

Re: [gmx-users] Fatal error: Number of atoms in Topology is not the same as in Trajectory

It is 15 ns of NPT equilibration and I have not got a proper npt output yet to go to the MDrun. Because when I run the -mdrun command, I get fatal error as water molecule can not be settled. I guess that the system might need more equilibration. These are the settings of my npt.mdp file.

Re: [gmx-users] error about pbc

@Justin, Fmax=8.0226669e+00 the system includes protein, lipid, water, ion Cl- em.mdp file is integrator = steep tinit= 0.0 dt = 0.02 nsteps = 5 nstcomm = 1 nstxout = 5000 nstvout

Re: [gmx-users] error about pbc

On 1/27/13 12:15 PM, Kieu Thu Nguyen wrote: @Justin, Fmax=8.0226669e+00 OK, that looks good. the system includes protein, lipid, water, ion Cl- em.mdp file is integrator = steep tinit= 0.0 dt = 0.02 nsteps = 5

[gmx-users] Extending NPT run

Dear advanced users, I'm trying determine the procedure for extending NPT run (i.e I realized the NPT run I did wasn't long enough, so I wish to run it for another million steps. ) what should I do to set up the run again continuing with the previous data? Thanks, Xu Dong Huang Chemical

Re: [gmx-users] Extending NPT run

On 1/27/13 9:49 PM, Xu Dong Huang wrote: Dear advanced users, I'm trying determine the procedure for extending NPT run (i.e I realized the NPT run I did wasn't long enough, so I wish to run it for another million steps. ) what should I do to set up the run again continuing with the previous

Re: [gmx-users] Extending NPT run

Thank you. I was just reading that as well, but didn't realize it could also be used to extend. I thought it was just runs that terminated early. Thanks Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Jan 27, 2013, at 9:51 PM, Justin

Re: [gmx-users] Extending NPT run

If I don't specify -extend (time) , will it automatically use the time step defined in the .tpr i'm using? Or should I just define the time anyway ? Thanks Xu Dong Huang Chemical Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Jan 27, 2013, at 9:54 PM, Xu

Re: [gmx-users] Extending NPT run

On 1/27/13 9:56 PM, Xu Dong Huang wrote: If I don't specify -extend (time) , will it automatically use the time step defined in the .tpr i'm using? Runs can be extended with -extend, -until, or with -nsteps. If you don't apply any of those, then yes, the number of steps in the .tpr file

Re: [gmx-users] error about pbc

Well, 20-30 fs is fine with Martini. But you may have to take care initially, and start with a smaller time step. Cheers, Tsjerk On Mon, Jan 28, 2013 at 3:11 AM, Justin Lemkul jalem...@vt.edu wrote: On 1/27/13 12:15 PM, Kieu Thu Nguyen wrote: @Justin, Fmax=8.0226669e+00 OK, that looks

[gmx-users] Steepest Descents converged to machine precision in 7559 steps, but did not reach the requested Fmax 100.

Dear Gromacs experts, I am running gromacs for the first time, and this is my em.mdp file. define = -DFLEXIBLE constraints = none integrator = steep dt = 0.01 ; ps ! nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb = 1.0 vdwtype = cut-off rvdw = 1.4 fourierspacing = 0.12

[gmx-users] making .top file of new LJ in Water

Dear gmx users I would like to start MD simulation for GAS Hydrate, consisting of TIP4P and LJ representing N2. I have made .top file by hand as following. When I use grompp_d for making .tpr file, I got the following error. However, LJ name in .gro file is same as in .top file, which is NX

RE: [gmx-users] making .top file of new LJ in Water

Hi Kenji, I guess if you change/swap the order of molecules in top file it will work. The order of molecules in your gro file should match up with your top file. If you give us more info it would be good :) I am just guessing :( [ molecules ] SOL 1088 LJN 1 Swap them like this

Re: [gmx-users] making .top file of new LJ in Water

Dear EB Thank you very much. Now, it works and looks OK to me. Regards Kenji - Original Message - From: Emanuel Birru emanuel.bi...@monash.edu To: 'Discussion list for GROMACS users' gmx-users@gromacs.org Date: 2013-01-28 14:04:37 Subject: RE: [gmx-users] making .top file of new

Re: [gmx-users] error about pbc

Thank Justin and Tsjerk so much for your help ! I will try smaller time step. And i hope it work :-) Regards, KT On Mon, Jan 28, 2013 at 10:19 AM, Tsjerk Wassenaar tsje...@gmail.comwrote: Well, 20-30 fs is fine with Martini. But you may have to take care initially, and start with a smaller

[gmx-users] Decreasing of the box size during membrane protein simulation

Dear Gromacs Users! I'm simulating membrane receptor embedded in the explicit membrane using charmm36 ff. My simulation setup consist of ; Compound#mols Protein 1 iso 1 POPC 228 SOL 11713 NA 66 CL 70 I've done