Re: [gmx-users] Positive potential energy

Hi, Even if there are minima on the surface that have negative energy (which will depend how the model was developed, which you should look into) there's no reason to expect an arbitrary starting configuration will find one after a steepest descent search. A tangled pile of strings will stay

Re: [gmx-users] How can I check external electric field was applied?

Thank you Dan, I used two graphene sheets with freeze and one sodium ion and one chloride ion are between them. It also had same ‘gmx potential’ result when simulated without graphene sheets. I’m now using Gromacs 5.1.4, using PME for Ewald summation with NVE ensemble for this test system.

[gmx-users] The PMF curve is asymmetric (However many results of membrane penetration are symmetric)

Hi all: I tried to use MD simulation to pull a drug across the POPC membrane and to calculate PMF. I obtained the PMF curve following the guide (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/) I found the PMF curve increases as the penetration process

[gmx-users] Positive potential energy

Hello, I want to simulate a box of polymer (32 chains) with salt. I started with one chain of the polymer in the box. However, after the energy minimisation, the energy is still positive. I found the discussion in the link below very similar to the problem I have:

Re: [gmx-users] g_sans calculation

I understand your pain, and the same could be said about gmx saxs as well. As Micholas said, CRYSON might be a good choice as far as implicit solvent methods go. Please notice that CRYSON is closed source, but it is well documented in the literature (it is basically a reimplementation of CRYSOL*).

Re: [gmx-users] g_sans calculation

>From what I understand very few people use the g_sans tool. One alternative is >to use CRYSON (if you are looking at biopolymers such as >proteins/dna/polysaccarides). Alternatively, SASSENA is also an option but it >has a lot of dependences. CRYSON:

[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

Re: [gmx-users] Potential energy coming out to be zero but not negative

Noone knows if you can continue your equilibration with this result, but it has nothing to do with the sign of the total energy. In the case of biomolecular forcefields involving quadratic energy terms for bonded stuff, the sign of the total energy is meaningless. _Reduction_ in total energy

[gmx-users] Potential energy coming out to be zero but not negative

Hello Sir, When I go for energy minimization for a protein complex containing 3 proteins, I obtain potential energy being minimized upto zero from positive. The potential energy is not becoming negative even after running for many steps as viewed in potential.xvg obtained after energy

Re: [gmx-users] antigen-antibody insilico MD using GROMACS

Deepak: Ag-Ab interactions occur via the hypervariable regions of the Ab. So the target amino acids for interaction will be much smaller. There are ample of docking softwares that can do this but that is a tricky affair at times. You may also look at protein-protein interaction softwares too.

Re: [gmx-users] Minimum compute compatibility

I wrongly downloaded the v5.0. It seems that 2018 version is better! Such error is now solved. Regards, Mahmood On Friday, February 23, 2018, 4:10:15 PM GMT+3:30, Mahmood Naderan wrote: Hi,While I set -DGMX_GPU=on for a M2000 card, the make returned an error

Re: [gmx-users] How can I check external electric field was applied?

Hi, You guessed correctly - gmx potential only calculates the electric field and potential of the system. It does not take into account the applied field. Are you using walls in your system? If so, are you using the 3DC correction along with PME for Ewald summation? If you answered yes to both

[gmx-users] How can I check external electric field was applied?

Dear Gromacs users, I’m testing a simple system that has one sodium ion and one chloide ion to check external electric field. ( Apply strong field along z axis, so I added the line of E_z = 1 10 0 to .mdp file. ) After a short simulation, I used ‘gmx potential’ to check the field. But the

Re: [gmx-users] antigen-antibody insilico MD using GROMACS

Hi, If you don't know where exactly binding occurs you can't really do this using only gromacs. I'd even suggest that until you have to, for antibodies it might be better to stick mostly to docking software. 1 - you have to have antibody and antigen parametrized using the same forcefield (FF). 2 -

[gmx-users] antigen-antibody insilico MD using GROMACS

Hi Gromacs users, I am studying antigen-antibody interaction at protein level. I have a protein sequence (no crystal structure, length 180 residues) of the antigen, and have predicted the secondary structure of it (and modeled). By performing conserved domain search using inferno and NCBI I found

[gmx-users] Minimum compute compatibility

Hi,While I set -DGMX_GPU=on for a M2000 card, the make returned an error which says compute_20 is not supported. So, where in the options I can drop the compute_20 capability? Regards, Mahmood -- Gromacs Users mailing list * Please search the archive at