Re: [gmx-users] Pressure coupling in expanded ensemble simulations

Hi Michael, I am just following up on your thoughts on how carrying out expanded ensemble at NVT and converting back to NPT on the mailing list. Again I appreciate your advice in this area. Best wishes, Gregory On 5/8/2019 12:01 PM, Michael Shirts wrote: Yeah, this is an unfortunately

Re: [gmx-users] water mediated Hbond

Thank you for your kind reply. - Message from Bratin Kumar Das <177cy500.bra...@nitk.edu.in> -     Date: Fri, 17 May 2019 13:33:30 +0530     From: Bratin Kumar Das <177cy500.bra...@nitk.edu.in> Reply-To: gmx-us...@gromacs.org Subject: Re: [gmx-users] water mediated Hbond       To:

Re: [gmx-users] Umbrella sampling PMF using pull-geometry=direction

I am sorry I forgot to give the link in the last mail. https://indianinstituteofscience-my.sharepoint.com/:f:/g/personal/pradyumn_iisc_ac_in/EkAdkzcZsepHvbE1UDJPS5UBg2mENMYsRC2S0Z2DDWS9xQ?e=3GeICo On Fri, May 17, 2019 at 5:03 PM Pradyumn Sharma < cherpradyumnsha...@gmail.com> wrote: > Dear all

[gmx-users] Umbrella sampling PMF using pull-geometry=direction

Dear all I am trying to get a PMF for a small molecule translocation through an asymmetric membrane. I am doing it using pull-geometry= direction to do umbrella sampling at each window. I am getting a profile in which PMF of molecule in the bulk water at one side of the membrane is different from

Re: [gmx-users] select an atom for "only" residue with make_ndx [ Resolved ]

Thanks Justin it worked. For the record, I have also found that 27 & a C31 C32 C33 is equivalent to a C31 | aC32 | aC33 & rLIPIDC or aC31 | aC32 | aC33 & 27. Note For the two latter commands the order of "r27 or rLIPIDC" is important Thanks again On 5/16/19 5:44 AM, ABEL Stephane

Re: [gmx-users] Rupture force definition

Dear Justin After long time again I want to ask one question. If suppose I want to repeat the same production simulation ( final md simulation) for different seeds, then how to do. Because as from the knowledge of gromacs there is no manual way to put different seeds in the .mdp files. On Mon,

Re: [gmx-users] water mediated Hbond

Hi, There are two types of hydrogen bond from dynamic point of view. 1) intermittent and 2) continuous. Between two type of hydrogen bond continuous h-bond autocorrelation will give you proper lifetime ...not intermittent. In gmx h-bond if we give the ACF of intermittent h-bond. Therefore it's

Re: [gmx-users] control parameter on the Lennard-Jones interactions

I have protein MD simulation file I want to find out protein water rdf with coordination number. Can anyone help regarding this? Thanks On Thu, May 16, 2019, 10:55 wrote: > > Dear gromacs members, > > I would ask you if in gromacs is possible to add a control parameter on > the Lennard-Jones