Re: [gmx-users] Type of function for bond or bend in SPC/E or TIP3P model

Thanks Mark. Could you send me the reference that SPC/E is a rigid model? I heard that SPC/E is a flexible model and I am doing simulation with gromacs and CP2K with this model without constraint. Regards, Leila On Mon, Feb 17, 2014 at 2:36 PM, Mark Abraham wrote: > Hi, > > Those water models a

Re: [gmx-users] Type of function for bond or bend in SPC/E or TIP3P model

Wikipedia seems to have these... http://en.wikipedia.org/wiki/Water_model. The authors of a technique using a version of SPC/E will have to have referred to the parameterization of that model, whether flexible or not. Mark On Tue, Feb 18, 2014 at 2:38 PM, leila salimi wrote: > Thanks Mark. >

[gmx-users] g_cluster failing

Hello GMX users, I hope you could help me solving this un-understandable (at least for me) error. I am trying to run g_cluster on one of my collected trajectories using the following command g_cluster -f allnj_1.xtc -n index.ndx -o -g -dist -ev -sz -tr -ntr -clid -cl -cutoff 0.5 -skip 10 -s ../a

[gmx-users] Nonsymetric molecule across pbc

Dear User, Can you please write me how to build a system of a protein (nonsymetric obviously) and place it in the on the box edge so that one half is within the unit cell and another one is copied across pbc on the other side? I assume I will get the error doing manually... please, advise. Steve

Re: [gmx-users] g_cluster failing

Building all-against-all matrices takes a lot of memory, and if it runs out, then crazy things happen. I suggest you start with versions of your trajectories sampled very sparsely so there are few tens of samples, and get a sane result from g_cluster from that. Then scale up / find a lot of memory

Re: [gmx-users] Nonsymetric molecule across pbc

On 2/18/14, 11:19 AM, Steven Neumann wrote: Dear User, Can you please write me how to build a system of a protein (nonsymetric obviously) and place it in the on the box edge so that one half is within the unit cell and another one is copied across pbc on the other side? I assume I will get the

Re: [gmx-users] Nonsymetric molecule across pbc

Thanks a lot! Can you please give me a hint how to apply umbrella sampling to the system of 4 nanotubes with pbc across xyz so that they infinite in length in z coordinate and 2 of them placed with its half to the unit cell copied across y coordinate... I want to see PMF minima (equilibrium distan

Re: [gmx-users] Nonsymetric molecule across pbc

On 2/18/14, 1:37 PM, Steven Neumann wrote: Thanks a lot! Can you please give me a hint how to apply umbrella sampling to the system of 4 nanotubes with pbc across xyz so that they infinite in length in z coordinate and 2 of them placed with its half to the unit cell copied across y coordinate..

Re: [gmx-users] Nonsymetric molecule across pbc

Thanks, The picture is confidential so I will send it to you in the separate msg. The distance between all tubes e.g. is 10 nm at the picture (I will attach polypeptides to them later on). So I want to run window at this distance... Then decrease it every 0.2 nm so all distances will decrease bet

[gmx-users] A new script to read hbmap from g_hbond

Dear GMX users , I uploaded a python script to the user contributions section of the GROMACS website (http://www.gromacs.org/Downloads/User_contributions/Other_software), it's called readHBmap.py. The idea behind the script is to allow the user to read the hydrogen bond map matrix file (.xpm)

Re: [gmx-users] Nonsymetric molecule across pbc

Or maybe just 2 of them in the box: so that the one in the cell and another one has its quarter in the unit cell edge and the free energy between them? Then this PMF take into account all of the others being copied around. Would US mdp option wont complain? Steven On Tue, Feb 18, 2014 at 7:49 PM

Re: [gmx-users] g_principal -- bug or very bad choice of filenames

On Fri, 7 Feb 2014, Justin Lemkul wrote: On 2/7/14, 6:08 PM, Antonio Baptista wrote: Dear all, This is a follow-up to an old thread on g_principal, which continues (as of version 4.6.5) to suffer from what I would call a bug or, at least, a very bad and misleading choice of output file name

Re: [gmx-users] g_principal -- bug or very bad choice of filenames

It shows as active to me... Mark On Tue, Feb 18, 2014 at 11:46 PM, Antonio Baptista wrote: > On Fri, 7 Feb 2014, Justin Lemkul wrote: > > >> >> On 2/7/14, 6:08 PM, Antonio Baptista wrote: >> >>> Dear all, >>> >>> This is a follow-up to an old thread on g_principal, which continues (as >>> of >>

Re: [gmx-users] g_principal -- bug or very bad choice of filenames

Szilárd already activated it a couple of hours ago (just noticed he replied to me only). The issue is already submitted also. Thanks anyway. Best, Antonio On Wed, 19 Feb 2014, Mark Abraham wrote: It shows as active to me... Mark On Tue, Feb 18, 2014 at 11:46 PM, Antonio Baptista wrote: O

[gmx-users] (Implicit solvation)Initial temperature changes to 0 K

I am trying to run a simulation of single Na ion in implicit solvent(water), with OPLSAA FF in gromacs 4.5.7. After running the simulation and viewing the .log file I find that the initial temperature is set to 0 K even though I have mentioned a ref_t as 300 K. Why does this happen? Any help is muc

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 118, Issue 73

Can any body explain how to calculate RMSD of only alpha helix and beta sheet of a protein in Gromacs -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mai