[gmx-users] Quick and Dirty Installation Error

Hello, I am trying to install GROMACS 2020 on my Windows laptop using Cygwin 3.1.4. I have run the steps outlined in the installation guide (http://manual.gromacs.org/documentation/2020/install-guide/index.html) before the command "make", version 4.3,. The command cmake in the build folder

[gmx-users] Electric field

Dear GMX users, I would like to perform MD simulations with external electric field. I would like to control the frequency. In the manual, I found that we should use ω 2.45 GHz, like microwave, and it was defined as ω=2πc/λ. I think that λ is equal to 0.1224 m. Finally, I think that ω =

Re: [gmx-users] gmx msd unusual unit

Thank you Justin and David, that's very helpful  -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se On Behalf Of David van der Spoel Sent: 16 March 2020 17:13 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] gmx msd unusual unit CAUTION: This email came

[gmx-users] makes sense for Ryckaert Bellemans dihs. only.

Dear Gromacs users I am calculating a dihedral angle between certain atoms by following command:- gmx angle -type dihedral -f md_1000ps.xtc -n dihedral.ndx -ov group.xvg -of trans.xvg Group 0 ( dihedral1) has 4 elements Group 1 ( dihedral2) has 4 elements Group 2 (

Re: [gmx-users] gmx msd unusual unit

Den 2020-03-16 kl. 15:10, skrev Justin Lemkul: On 3/16/20 10:07 AM, Joe Paul-Taylor wrote: Hello With running gmx msd I am told in the output the y axis unit is nm/ S2/ N, which is unexpected. Is this simply an print error or is there an error within the calculation? I have provided a copy

Re: [gmx-users] energy minimization in vacuum

Hi, If u minimise the protein in vaccum...the bad contact within the protein atoms will be removed After solvation if u do...then both the bad water contact and steric clashes within the protein will be removed. On Mon 16 Mar, 2020, 8:37 PM Deepanshi ., wrote: > Dear all, > > I am trying

[gmx-users] energy minimization in vacuum

Dear all, I am trying to simulate an all atom protein in water. I wanted to ask that what is the importance of minimizing the protein in a vacuum. It is not mentioned in the lysozyme tutorial. Thanks. Regards, Deepanshi -- Gromacs Users mailing list * Please search the archive at

[gmx-users] gmx msd unusual unit

Hello With running gmx msd I am told in the output the y axis unit is nm/ S2/ N, which is unexpected. Is this simply an print error or is there an error within the calculation? I have provided a copy of the output below, noting the units of the self-diffusion coefficient are sensible. Any

Re: [gmx-users] gmx msd unusual unit

On 3/16/20 10:07 AM, Joe Paul-Taylor wrote: Hello With running gmx msd I am told in the output the y axis unit is nm/ S2/ N, which is unexpected. Is this simply an print error or is there an error within the calculation? I have provided a copy of the output below, noting the units of the

Re: [gmx-users] Fatal error: Too many warnings (3) ; WARNING * [file lig.prm, line **] :: How to overcome this error -> simply delete the lines which give warnings?

On 3/15/20 6:39 PM, Adarsh V. K. wrote: Dear all, How to overcome this error ? How to overcome this error. Simply delete the lines which give warnings? *gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr -maxwarn 1* The above command returns following 'error message' while using

Re: [gmx-users] (no subject)

Download and use the forcefield files from the ATB server website, and then make that you correctly point to it in your top file. On Sat, 14 Mar. 2020, 7:32 pm FAISAL NABI, wrote: > Hi, > I have been a new user and i was following the protein-ligand complex > tutorial for MD. I have used

Re: [gmx-users] Can you help regarding this

What specifically do you need help with? Both the error messages there are explicit about what the issues are, first you have failed to correctly adjust the number of molecules of the topology (.top) to match the coordinate file. You also have a +10 net charge, which is unlikely to be a good idea.

Re: [gmx-users] Creating a simple water box

Is the "close contact" really an issue? As soon as you start any sort of MD that will quickly adjust itself. On Sat, 14 Mar. 2020, 7:23 pm dodia, wrote: > Dear gromacs users, > > I was trying a simple gmx solvate test on a water box of size 25*20*20 > angstrom, creating a water box of density 1

[gmx-users] Fwd: Problems with Non-equilibrium MD

Hi all, I am using non-equilibrium MD to calculate the viscosity of the liquid by applying a shear on xy direction. My problem is that when I observe the trajectory of the simulation, I find only the box deformed and particles did not change correspondingly, as shown in the attached image. I

Re: [gmx-users] Fwd: Problems with Non-equilibrium MD

Hi Jun, Can you add a link to your image online rather than attaching it? Benson On Mon, Mar 16, 2020, at 10:25 AM, Jun Zhou wrote: > Hi all, > > I am using non-equilibrium MD to calculate the viscosity of the liquid by > applying a shear on xy direction. My problem is that when I observe the

Re: [gmx-users] no subject

Hello Faisal, Easiest way to do this is by navigating to the MD files tab and download the "Gromacs 4.5.x-5.x.x 54a7" below this warning - "*Warning!* This molecule contains non-standard atom types not included in the standard GROMOS 54A7 forcefield..." The folder contains the procedure to