[gmx-users] force calculations in PMF calculations

Dear Gromacs users I had a doubt regarding pull code. Which force values are considered while calculations? ensemble average values of the entire system or the forces acting on the group/atoms under consideration. Regards -- Deepak U. Bapat -- Gromacs Users mailing list * Please search the a

[gmx-users] force calculations in PMF

Dear Gromacs users I had a doubt regarding pull code. Which force values are considered while calculations? ensemble average values of the entire system or the forces acting on the group/atoms under consideration. Regards Deepak -- Gromacs Users mailing list * Please search the archive at ht

Re: [gmx-users] force calculations in PMF

, Jan 4, 2017 at 8:46 AM, Alex wrote: > There's a reason no one is replying: we can't understand your question. :) > > > > On 1/3/2017 8:09 PM, deepak bapat wrote: > >> Dear Gromacs users >> >> I had a doubt regarding pull code. >> >> Whic

Re: [gmx-users] force calculations in PMF

he objective is to artificially move > one subsystem relative to another. > > This assumes I understood your question. :) > > Alex > > > > On 1/3/2017 8:22 PM, deepak bapat wrote: > >> HI Alex! >> >> >> >> OK.. :-) >> >> Let me

Re: [gmx-users] force calculations in PMF

ally move one subsystem relative to >> another. >> >> This assumes I understood your question. :) >> >> Alex >> >> >> On 1/3/2017 8:22 PM, deepak bapat wrote: >> >>> HI Alex! >>> >>> >>> >>> OK.. :-)

[gmx-users] regarding Lorentz-Berthelot mixing rules

Dear gmx-users, Is it possible to use customized Lorentz-Berthelot rules? In one of the research articles i found that LB factors were modified by multiplying by a constant value. How can i incorporate such changes in my mdp file? -- Deepak -- Gromacs Users mailing list * Please search the

Re: [gmx-users] regarding Lorentz-Berthelot mixing rules

Dear David and Mark Thank you. Deepak On Thu, Apr 14, 2016 at 5:34 PM, Mark Abraham wrote: > Hi, > > On Thu, Apr 14, 2016 at 1:05 PM deepak bapat wrote: > > > Dear gmx-users, > > > > Is it possible to use customized Lorentz-Berthelot rules? > > > Not

[gmx-users] Modify source file for specific use

Dear GMX users I wanted to modify gmx freevolume code for my usage. I found the source code on the following link https://github.com/gromacs/gromacs/blob/master/src/gromacs/trajectoryanalysis/modules/freevolume.cpp Now I want to change this code slightly for my use and implement to analyze the t

Re: [gmx-users] Modify source file for specific use

Dec 22, 2017 at 12:25 AM deepak bapat wrote: > > > Dear GMX users > > > > I wanted to modify gmx freevolume code for my usage. > > I found the source code on the following link > > > > > > https://github.com/gromacs/gromacs/blob/master/src/ > gromacs/tra

[gmx-users] widom TPI insertion

Dear Gromacs Users I have carried out TPI inserion of small LJ particle in SPC/E water. NPT ensemble was used. 1 bar, 300 K. 3 nm box was used for simulation without test particle. LJ parameters of the TPI particle were 9e-02 and 6.51e-02. Successful insertion probability is around 18%. tpi.xvg f

[gmx-users] Free energy of VDW transformation from state A to State B

Dear gmx-users I am trying to calculate free energy of VDW transformation. The system is very simple as I want to test the methodology. Single neutral LJ particle is transformed from state A to state B in TIP4P water. I have tried simulations with different state B LJ parameters without changing

[gmx-users] Thermodynamic integration of VDW transformation

Dear Gromacs users I had posted a similar question recently, but I did not get any reply so I think I did not put it correctly. It is regarding thermodynamic integration of mutating (not decoupling ) VDW parameters from state A to state B. Will different state B parameters have different values

[gmx-users] .mdp file settings for thermodynamic integration

Dear Gromacs users I had a doubt regarding .mdp options for free energy using constrained dynamics. If i wish to change a bond length from l_A to l_B (say for example from 0.5 nm to 5 nm. this bond will be used in the form of constraints type 2. something similar to what is shown in manual of gr

[gmx-users] Suggestion for workstation configurations

Dear Gromacs Users Can you please suggest which configuration should be prefered for Gromacs 1) DUAL intel Xeon ES-2620 v4 2.1 GHZ, 3.0GHz Turbo, 2113 MHz, 20MB, 8SW NVIDIN Quadro P5000 16 GB (4 DP, DL-DVI-D) 64 GB 2400 DDR4 Cost ~ 5400 USD 2) Intel Xeon ES-1660 v4 (8C, 3.2 GHz, 3.8 GHz turbo

[gmx-users] non zero free energy values in mass transformation

Dear Gmx Users I am trying to find out free energy of transforming one neutral LI to one CL in aqueous solution. Water model is SPC/E. Gromacs version: 5.1.2 I am doing something like this Insert 1 Li olecule in water. (Li parameters were taken from Kasper P. Jensen and William L. Jorgensen 20

Re: [gmx-users] non zero free energy values in mass transformation

effects would have to be added afterwards, > > assuming that some analytical result could be computed) > > > > I hope it helps > > > > Andre > > > > On Fri, Aug 11, 2017 at 6:36 AM, deepak bapat wrote: > > > > > Dear Gmx Users > > >

Re: [gmx-users] non zero free energy values in mass transformation

/mol). So I am still worried about this non zero behavior. Thanks and regards Deepak On Sat, Aug 12, 2017 at 10:11 AM, deepak bapat wrote: > Thank you Andre and Dan. > > I'll read more about. > > Deepak > > On Fri, Aug 11, 2017 at 7:35 PM, Dan Gil wrote:

Re: [gmx-users] non zero free energy values in mass transformation

h, I am also working on a very similar problem without > success (yet). I am very curious to see if this works out for you. > > Dan > > > On Sun, Aug 13, 2017 at 11:08 PM, deepak bapat wrote: > > > Hi > > > > To study the efect of particle mass on excess chemic

[gmx-users] Topology file (type A type B format) for free energy calculation of bond breaking

Dear Gromacs Users I wish to calculate free energy simulation in which I wish to break bond within a molecule from state A to state B. If I use bond type 6 to define that bond in the molecule then i think it should not generate exclusions (as stated in the manual of Gromacs version 5.1.2, sectio