Re: [gmx-users] pressure and temperature coupling is off in vacuum simulations

On 9/23/15 6:37 AM, Erik Marklund wrote: On 23 Sep 2015, at 08:28, Mark Abraham > wrote: Hi, On Wed, Sep 23, 2015 at 8:32 AM tasneem kausar > wrote: Dear Gromacs users I

Re: [gmx-users] pressure and temperature coupling is off in vacuum simulations

> On 23 Sep 2015, at 12:35, Justin Lemkul wrote: > > > > On 9/23/15 6:37 AM, Erik Marklund wrote: >> >> On 23 Sep 2015, at 08:28, Mark Abraham >> > wrote: >> >> Hi, >> >> On Wed, Sep 23, 2015 at 8:32 AM tasneem

Re: [gmx-users] g_mmpbsa

Dear Leila IF you want help, you must say it best Cris 2015-09-21 7:00 GMT-03:00 leila karami : > Dear gromacs users, > > Can I use g_mmpbsa tool for calculation of binding free energy in > RNA-ligand complex? > > Best, > Leila Karami > -- > Gromacs Users mailing list >

Re: [gmx-users] pressure and temperature coupling is off in vacuum simulations

Dear gmx Users i am doing a simulation for my experiments. how can i produce mdp file? Best regards -- 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

Re: [gmx-users] pressure and temperature coupling is off in vacuum simulations

On 23 Sep 2015, at 08:28, Mark Abraham > wrote: Hi, On Wed, Sep 23, 2015 at 8:32 AM tasneem kausar > wrote: Dear Gromacs users I have performed MD simulation for protein in

Re: [gmx-users] pressure and temperature coupling is off in vacuum simulations

Hi, True, there can be cases where a vacuum simulation is a useful model of reality. :-) Mark On Wed, Sep 23, 2015 at 12:38 PM Erik Marklund wrote: > > On 23 Sep 2015, at 08:28, Mark Abraham > wrote: > > Hi, > >

Re: [gmx-users] pressure and temperature coupling is off in vacuum simulations

If you want to ask a new question, please send a new message and don't hijack an unrelated topic. On 9/23/15 7:39 AM, aghaei.arsalan wrote: Dear gmx Users i am doing a simulation for my experiments. how can i produce mdp file? It's a text file. Write it with a plain text editor.

Re: [gmx-users] PMF calculation_ Constraint

Dear Justin. Thanks for response. I used constraint method because I wanted to calculate MSD, How does using a bigger box helps me? because when I make box bigger, I need to run a little bit to equilibrate system, and again the tocopherol can move and come out of the box. On Tue, Sep 22, 2015 at

[gmx-users] mdp files

Hi all, I am running CGMD simulation of a membrane protein in DPPC with Martini FF. I just want to check if these mdp files are correct. I would appreciate if you take a look and tell me if there is something wrong or missing. <*minimization.mdp*> integrator = steep dt =

Re: [gmx-users] Free energy perturbation with hamiltonian replica exchange (FEP - HEX)

I would like to add that the manual is not correct for expanded free energy calculations (under Gromacs 5.0.6). The manual states the parameters with the following options: *lmc-stats*: no, metropolis-transition, barker-transition, wang-landau, min-variance *lmc-mc-move*: no,

Re: [gmx-users] pressure and temperature coupling is off in vacuum simulations

Hi, On Wed, Sep 23, 2015 at 8:32 AM tasneem kausar wrote: > Dear Gromacs users > > I have performed MD simulation for protein in vacuum condition. That's super artificial, so nothing else you do matters :-) I have seen > papers where people are putting the pressure

Re: [gmx-users] To calculate temperture in a specific region

Hi, Yes, you would need a dynamic selection, so that your geometric criterion is implemented every time step that you want to average, and then somehow cope with the fluctuating numbers of particles selected. gmx select can create such a thing, but few other GROMACS tools can use it without you

Re: [gmx-users] To calculate temperture in a specific region

Thanks you very much mark. I will try as you suggested. -Original Message- From: Krishna Mohan Gupta Sent: Wednesday, September 23, 2015 10:14 AM To: 'gmx-us...@gromacs.org'; 'gromacs.org_gmx-users@maillist.sys.kth.se' Subject: RE: [gmx-users] To calculate temperture in a specific region

[gmx-users] NPT with implicit solvent

hi gmx users,i am running an implicit solvent simulation and i get error with NPT. i checked different tutorials and no one used NPT with implicit solvent. may i know the reason of why not using equilibration with implicit. thanks in advance. Regards Sana Saeed -- Gromacs Users mailing list *

[gmx-users] COM motion removal

Hey gromacs users, When COM motion should be used in simulation? I followed in justin lemkul's gromacs tutorials of gromacs in internet. I found that he did not use COM motion removal in some of the simulation. Can any body tell me should i use and when should not? Regards Masrul -- Gromacs