[gmx-users] vdW cut-off to LJPME: Simulation crashes immediately

after a few steps. Even decreasing the time-step to 0.5 femtoseconds doesn't lead to a stable simulation.Has anyone encountered similar problem? I appreciate your input. The version i am using is *gromacs-2018.3*. Thank you, Udaya Dahal -- Gromacs Users mailing list * Please search the archi

[gmx-users] vdW cut-off to LJPME: Simulation crashes immediately

after a few steps. Even decreasing the time-step to 0.5 femtoseconds doesn't lead to a stable simulation.Has anyone encountered similar problem? I appreciate your input. The version i am using is *gromacs-2018.3*. Thank you, Udaya Dahal -- Gromacs Users mailing list * Please search the archi

[gmx-users] protonation free energy: parameter setting

Hi Everyone, I am trying to estimate the protonation free energy using TI. My thermodynamic cycle is : a) VDW0 Q0 --> VDW1 Q0 b) VDW1 Q0 --> VDW1 Q1 I put varying lambda for "vdw_lambdas" and zeros for all "coul_lambdas" for step *a* and "vdw_lambdas=1" and varying "coul_lambdas" for step *b*. M

[gmx-users] g_sans calculation

Dear Gromacs Users, I am calculating the g_sans in the simulation but I am not able to find how it is calculated. The help content is minimal. I am just wondering if anyone has looked into how it is calculated (any reference to algorithm?). Regards, -- Gromacs Users mailing list * Please searc

Re: [gmx-users] Double counting of h-bonds g_hbond:issue

Thanks Justin. It was the merging of the hbonds data that led to show the repetition of the list. If we do nomerge everything is reasonable. On Wed, Feb 18, 2015 at 7:41 AM, Justin Lemkul wrote: > > > On 2/17/15 5:14 PM, Udaya Dahal wrote: > >> Thanks Justin for prompt

Re: [gmx-users] Double counting of h-bonds g_hbond:issue

mentioned Polymer water h-bonds. On Tue, Feb 17, 2015 at 7:58 AM, Justin Lemkul wrote: > > > On 2/16/15 7:39 PM, Udaya Dahal wrote: > >> Hi All, >> >> When I used the g_hbond the hydrogen bonding i was getting was quite good >> but when I checked the index file

[gmx-users] Double counting of h-bonds g_hbond:issue

Hi All, When I used the g_hbond the hydrogen bonding i was getting was quite good but when I checked the index file i find double counting of the bonds. So far, it seems to me that g_hbond is giving higher than the real hydrogen bonds present in the system. For eg. in the following OW-HW-oxygen, w

[gmx-users] Simulation Crash

​​I have a polymer and water simulation. Since I am using the buckingham and the LJ potential, I am using the table for the non bonded pairwise interaction. The system blows up. Since the starting configuration matters a most for the simulation, I used packmol to generate the starting structure and

Re: [gmx-users] Error with tabulated potential and tip4p water model

Start with a single polymer > solvated, then perhaps use genconf to add complexity. > > Mark > > > On Mon, Aug 4, 2014 at 8:48 AM, Udaya Dahal wrote: > > > It was immediate. But I figured out the way to solve that issue. Looks > > like the starting initial configur

[gmx-users] Warning in the Tabulated potential.

My potential function is little different from the general LJ and Buckingham potential. Thus instead creating a single table for r,f,-f',g,-g',h,-h'; I combined all the potential and made f,-f',h,h'=0 and put the total potential and their derivatives on g and g'. While running the energy minimizat

Re: [gmx-users] Error with tabulated potential and tip4p water model

9:23 PM, Mark Abraham wrote: > Immediately, or after some EM steps? > > Mark > > > On Sun, Aug 3, 2014 at 12:56 PM, Udaya Dahal > wrote: > > > I have tabulated potential for all the possible combinations(non > bonded). > > I am using Tip4p water mo

[gmx-users] Error with tabulated potential and tip4p water model

I have tabulated potential for all the possible combinations(non bonded). I am using Tip4p water model for the polymer water interaction. While running the energy minimization i got the error like below. Fatal error: Settle block crossing node boundaries constraint between atoms 664, 665, 666) Fo

[gmx-users] Problem with T-coupling.

h the email in google drive.​ eq.mdp <https://docs.google.com/file/d/0ByXdaXpbCwOyUVJuOFZ4dFBaa1U/edit?usp=drive_web> ​This one is for Berendsen T coupling. ​ eq_nh.mdp <https://docs.google.com/file/d/0ByXdaXpbCwOySnBIa2tLRkFPZGc/edit?usp=drive_web> ​This one is for Nose-hoover.

Re: [gmx-users] Degree of hydrogen bonding

m.xvg file, the second column represent hydrogen bonds and the third column represents the pairs within 0.35nm. what does pair represent over here? Does it mean two h-bonds or donor acceptor number? Thank you, On Thu, May 8, 2014 at 4:24 PM, Udaya Dahal wrote: > Thank you. > > > On Th

Re: [gmx-users] Degree of hydrogen bonding

ess you want to drown > while interpreting -hbn and -hbm. > > Mark > > > On Thu, May 8, 2014 at 5:21 PM, Udaya Dahal wrote: > > > Thank you Justin for quick reply. I did exactly what you have mentioned > but > > the thing is I am getting number of hydrogen bonds per

Re: [gmx-users] Degree of hydrogen bonding

indexing so that I can compare the visual image to that number. On Tue, May 6, 2014 at 10:48 PM, Justin Lemkul wrote: > > > On 5/6/14, 6:05 PM, Udaya Dahal wrote: > >> Hi all, >> >> I am simulating a PPO chain in water. I am looking for the degree of >> hydration

[gmx-users] Degree of hydrogen bonding

is the atomistic one and and the water i am using is spce. Also how do the boundary bonds are calculated since for a small box, the omission of the boundary bonds will completely alter the property. Regards, Udaya Dahal -- Gromacs Users mailing list * Please search the archive at http