Re: [gmx-users] Index file regarding

It's 'r37-70 | r 120-167 | ...' so on and so forth. On Mon, May 7, 2018 at 12:06 PM RAHUL SURESH wrote: > Dear all, > > My protein structure has 400 residues of which I want to calculate RMSD of > particular 200 residues (approx) and they are not continuous. For

Re: [gmx-users] Index file regarding

group alone.. So what group should i select? > > On Mon, May 7, 2018 at 6:50 PM, RAHUL SURESH <drrahulsur...@gmail.com> > wrote: > > > thank you. > > > > On Mon, May 7, 2018 at 3:39 PM, Shreyas Kaptan <shreyaskap...@gmail.com> > > wrote: > > >

Re: [gmx-users] free energy landscape

Sounds like a problem for string methods. However, it's hard to judge without actually looking at what you have. Cheers. On Sun, May 13, 2018 at 3:47 PM Rezgar Pakravan wrote: > ​HI there > > I got free energy landscape using Mathematica software to get coordinates >

Re: [gmx-users] replicates with different random seed

If you use the .cpt file then the velocities will be provided as from the checkpoint. This would effectually only lengthen the simulation. In order to truly sample the simulation space from a "random" seed, you should reassign velocities from scratch as in the .mdp file. In *principle* the

Re: [gmx-users] membrane-protein system by using charmm36 ff

pare+protein) using NVT followed by > NPT ensemble before production of MD simulation? > Thank you all for your help. > > > Olga > > > > > 2018-06-17 15:34 GMT+03:00 Shreyas Kaptan : > > > Hi. > > > > Maybe you already know this but you can also

Re: [gmx-users] About the "g_contacts" program for gromacs

In the paper it mentions that: This paper and its associated computer program are available via the Computer Physics Communication homepage on ScienceDirect ( http://www.sciencedirect.com/science/journal/00104655). Hope that helps. On Thu, Jun 14, 2018 at 5:53 PM ABEL Stephane wrote: > Hi

Re: [gmx-users] High pressure

That is indeed strange. Could it be because of the compressibility = 0 in the first coordinate direction? if your simulations start with a badly adjusted (minimized) structure in the TPR then it might get stuck there because the 0 compressibility might not allow any change in the box dimensions

Re: [gmx-users] High pressure

stem in such situation? > > Regards, > Alex > > On Wed, Jun 13, 2018 at 5:30 PM, Shreyas Kaptan > wrote: > > > That is indeed strange. Could it be because of the compressibility = 0 in > > the first coordinate direction? if your simulations start with a badly > > a

Re: [gmx-users] membrane-protein system by using charmm36 ff

Hi. Maybe you already know this but you can also build the whole embedded system with charmm-gui. Also, your parameters appear reasonable to me at first glance. As for the equilibration, that is a system specific question. If you have a "simple" uniform lipid content in the bilayer I would say

Re: [gmx-users] Cavity in the system after NVT equilibration

The cavity, which is due to negative pressure in the system, might imply one of the two things: The Box is too big for the system or that the MD simulation implodes the system somehow. I have seen issues like these when the system is not well minimized and has some obvious artefacts like "broken"

[gmx-users] Essential dynamics

Dear All, I have a question regarding the make_edi tool. I used it some time back to restrain my structures to a particular projection value of an eigen vector with the -restrain keyword. However, I seem to have forgotten how to set the value of the projection in the .edi file. Does anyone here

Re: [gmx-users] Essential dynamics

Thanks a lot, Carsten!!! Exactly what I needed :). Shreyas On Tue, Jun 26, 2018 at 3:41 PM Kutzner, Carsten wrote: > Hi Shreyas, > > > On 26. Jun 2018, at 15:21, Shreyas Kaptan > wrote: > > > > Dear All, > > > > I have a question regarding the

Re: [gmx-users] [EXT] Re: Updated tutorials and new website

Dear Iris, that sounds like a great idea. I would like to ask what topics would be considered useful for tutorials. I can think of a few: 1. Fast thermodynamic integration for alchemical transformations with the CGI method with hybrid topologies for more complex examples 2. Replica exchange

Re: [gmx-users] Updated tutorials and new website

Hi Justin, that sounds like a great plan. Thanks for initiating something like this. Iris, I am up for helping with some of the tutorials, especially, the ED simulations if you need any help. That is something I have some experience with as well. Shreyas On Tue, Jul 3, 2018 at 1:13 PM Justin

Re: [gmx-users] gmx potential

available to the public in any way. > > Alex > > > > On 3/22/2018 4:59 AM, Shreyas Kaptan wrote: > >> Okay. But then how can one confirm that the correct potential is applied >> if >> not by looking at the charge distribution? >> >> Shreyas >

Re: [gmx-users] gmx potential

quot;the applied field was blah blah > on step x" that still wouldn't mean anything unless the other output is > consistent. > > Mark > > On Mon, Apr 2, 2018, 15:01 Shreyas Kaptan <shreyaskap...@gmail.com> wrote: > > > Hi. > > > > Can anyone else t

Re: [gmx-users] gmx potential

ial drop due to >> external electric field itself. What it does instead is described in the >> utility documentation. >> >> Alex >> >> >> On 3/21/2018 12:42 PM, Shreyas Kaptan wrote: >> >>> Dear GMX users, >>> >>> I am trying to

Re: [gmx-users] gmx potential

rom one end to the other, but that is purely artificial. I stay > away as much as possible from plotting charge distributions from > simulations steered by external fields. > > Alex > > On Wed, Mar 21, 2018 at 4:29 PM, Shreyas Kaptan <shreyaskap...@gmail.com> > wrote: &g

[gmx-users] gmx potential

Dear GMX users, I am trying to use the gmx potential tool to calculate the potential created by applying a constant electric field in the Z-direction. I am using the 2018 gromacs version. The electric field was applied with: electric-field-z = 0.00625 0 0 0; 0.1 V voltage for 160

Re: [gmx-users] gmx potential

ctly what it says it does. Which part is misunderstood? > > Alex > > On Wed, Mar 21, 2018 at 3:51 PM, Shreyas Kaptan <shreyaskap...@gmail.com> > wrote: > > > Hi. > > > > Thanks for the reply! Maybe I misunderstood the tool documentation. So > what > >

Re: [gmx-users] tilt angle

If you fire the 'gmx make_ndx' you will find that there is a section there for c-alpha atoms. By combining the c-alpha group with the index of the protein with the "&" operator (without quotations) should work. On Wed, Jun 20, 2018 at 8:41 AM Fa Hamedi wrote: > Hi, > I am new in this mailing

Re: [gmx-users] Non-symmetric PMF across lipid bilayer

I am reasonably sure that if the bilayer composition is asymmetric with respect to leaflets you should see asymmetry in the PMF. In the ideal case, of infinite sampling, you should have zero free energy difference in the bulk solvent for either side. On Wed, Nov 21, 2018 at 2:52 PM Gmx QA wrote:

Re: [gmx-users] Coulomb and vdW energies

Hi. I would not say that it is completely unrealistic/unphysical. Especially, the Electrostatic part. If within two subgroups, you could show that there is systematic repulsive or attractive potential, that could lead to some hypothesis about how they interact (e.g. pushing/pulling). Of course,