[gmx-users] Cannot find position restraint file restraint.gro

Hi, I have been trying to simulate isobutane in urea as a solvent. I have made myself urea.itp and urea.gro file for charmm36 forcefield under equilibrating at certain temperature and pressure. First nvt followed by npt I got error like this while equilibriating. Program: gmx grompp, version

[gmx-users] MDP define in GROMACS 2018

Hi all, I am excited to try out the new PME code in GROMACS 2018! It seems that preprocessor variables can no longer be given values in the MDP as of GROMACS 2018? So in 2016 I could do define = -DPOSRES -DPOSRESFC=500.0 and then in the posres ITP: #ifndef POSRESFC #define POSRESFC 1000.0

[gmx-users] Is there any difference with gromacs and other MD programs?

Dear gmx users, I’ve started to run MD simulation of ion aggregation of aqueous solution. (JCP 145, 174501 (2016)) So I followed adding initial molecules(I gained BF4 ion topology from https://atb.uq.edu.au/molecule.py?molid=26889) , em, ensembles and md simulation. Then I calculated RDF but

Re: [gmx-users] SDS initial setup

A visualisation to help see what is going on with the PBC and the molecules https://twitter.com/dr_dbw/status/909559339366572032 Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052

[gmx-users] huge center of mass distance mismatch in umbrella sampling

Hi, I have two copies of a protein that are in contact with each other. Their center of mass distance is about 5.5 nm. However, in the resulting potential of mean force, there is an energetic minimum at 3.5 nm. How is this at all possible? At that distance half of the protein would be

Re: [gmx-users] inter- and intra-molecular hbond analysis

Hi Gromacs users, I would like to know your opinion on this. Thanks in advance for your comments Cheers, Mohsen On Fri, Jan 19, 2018 at 5:16 PM, Mohsen Ramezanpour < ramezanpour.moh...@gmail.com> wrote: > Dear Gromacs users, > > Given a mixed bilayer composed of two lipids (type A and B), I

Re: [gmx-users] gmx dipole and gmx potential

Den 2018-01-21 kl. 14:27, skrev ali akgün: Hİ all I am newbie and GROMACS, I did some dipole moment and electric potential calculation for water solutions. I want to understand gmx dipole and gmx potential algorithm.I read GROMACS manual 8.5.4 and 8.5.3 but I can not understand about gmx

Re: [gmx-users] KALP15 in DPPC

hi . in vmd how can i find special number for each atom? i want to delete those atoms from my gro file. tnx On Mon, Jan 15, 2018 at 9:12 PM, Justin Lemkul wrote: > > > On 1/15/18 10:56 AM, negar habibzadeh wrote: > >> tnx so much >> i got nvt.tpr and now i want to run it but

[gmx-users] disulfide bond missing even with -ss

Hi, If your are not sure that SS is formed or taken into account in the top file,. You could do a short minimization of the initial structure and observe the minimized structure has the SS bond. If it also a good way to see if the top file is correct. Sté

Re: [gmx-users] disulfide bond missing even with -ss

On 1/21/18 11:42 AM, MD wrote: On Sun, Jan 21, 2018 at 11:33 AM, Justin Lemkul wrote: On 1/21/18 11:30 AM, MD wrote: On Sun, Jan 21, 2018 at 11:22 AM, Justin Lemkul wrote: On 1/21/18 11:20 AM, MD wrote: On Sun, Jan 21, 2018 at 11:05 AM, Justin

Re: [gmx-users] disulfide bond missing even with -ss

On Sun, Jan 21, 2018 at 11:33 AM, Justin Lemkul wrote: > > > On 1/21/18 11:30 AM, MD wrote: > >> On Sun, Jan 21, 2018 at 11:22 AM, Justin Lemkul wrote: >> >> >>> On 1/21/18 11:20 AM, MD wrote: >>> >>> On Sun, Jan 21, 2018 at 11:05 AM, Justin Lemkul

Re: [gmx-users] disulfide bond missing even with -ss

On 1/21/18 11:30 AM, MD wrote: On Sun, Jan 21, 2018 at 11:22 AM, Justin Lemkul wrote: On 1/21/18 11:20 AM, MD wrote: On Sun, Jan 21, 2018 at 11:05 AM, Justin Lemkul wrote: On 1/21/18 10:59 AM, MD wrote: On Sun, Jan 21, 2018 at 10:49 AM, Justin

Re: [gmx-users] disulfide bond missing even with -ss

On Sun, Jan 21, 2018 at 11:22 AM, Justin Lemkul wrote: > > > On 1/21/18 11:20 AM, MD wrote: > >> On Sun, Jan 21, 2018 at 11:05 AM, Justin Lemkul wrote: >> >> >>> On 1/21/18 10:59 AM, MD wrote: >>> >>> On Sun, Jan 21, 2018 at 10:49 AM, Justin Lemkul

Re: [gmx-users] disulfide bond missing even with -ss

On 1/21/18 11:20 AM, MD wrote: On Sun, Jan 21, 2018 at 11:05 AM, Justin Lemkul wrote: On 1/21/18 10:59 AM, MD wrote: On Sun, Jan 21, 2018 at 10:49 AM, Justin Lemkul wrote: On 1/21/18 10:46 AM, MD wrote: On Sun, Jan 21, 2018 at 10:37 AM, Justin

Re: [gmx-users] disulfide bond missing even with -ss

On Sun, Jan 21, 2018 at 11:05 AM, Justin Lemkul wrote: > > > On 1/21/18 10:59 AM, MD wrote: > >> On Sun, Jan 21, 2018 at 10:49 AM, Justin Lemkul wrote: >> >> >>> On 1/21/18 10:46 AM, MD wrote: >>> >>> On Sun, Jan 21, 2018 at 10:37 AM, Justin Lemkul

Re: [gmx-users] disulfide bond missing even with -ss

On 1/21/18 10:59 AM, MD wrote: On Sun, Jan 21, 2018 at 10:49 AM, Justin Lemkul wrote: On 1/21/18 10:46 AM, MD wrote: On Sun, Jan 21, 2018 at 10:37 AM, Justin Lemkul wrote: On 1/21/18 10:29 AM, MD wrote: I modified the specbond.dat and change the

Re: [gmx-users] disulfide bond missing even with -ss

On Sun, Jan 21, 2018 at 10:49 AM, Justin Lemkul wrote: > > > On 1/21/18 10:46 AM, MD wrote: > >> On Sun, Jan 21, 2018 at 10:37 AM, Justin Lemkul wrote: >> >> >>> On 1/21/18 10:29 AM, MD wrote: >>> >>> I modified the specbond.dat and change the cutoff to be

Re: [gmx-users] disulfide bond missing even with -ss

On 1/21/18 10:46 AM, MD wrote: On Sun, Jan 21, 2018 at 10:37 AM, Justin Lemkul wrote: On 1/21/18 10:29 AM, MD wrote: I modified the specbond.dat and change the cutoff to be 2.04A, still nothing... Please don't spam the list with minute-by-minute updates. ​ sorry ​for

Re: [gmx-users] disulfide bond missing even with -ss

On Sun, Jan 21, 2018 at 10:37 AM, Justin Lemkul wrote: > > > On 1/21/18 10:29 AM, MD wrote: > >> I modified the specbond.dat and change the cutoff to be 2.04A, still >> nothing... >> > > Please don't spam the list with minute-by-minute updates. > ​ sorry ​for the scattered

Re: [gmx-users] Why gyration radius keep dropping?

On 1/19/18 1:22 PM, ZHANG Cheng wrote: Dear Gromacs, I am running MD at 500 K for my protein. I used this to analyse the gyration radius echo 1 | gmx gyrate -s md_0_1.tpr -f md_0_1_noPBC.xtc -o gyrate.xvg I thought the radius should keep increase, as the protein unfolds at high

Re: [gmx-users] -inter command

On 1/20/18 2:26 AM, za...@tezu.ernet.in wrote: Message: 1 Date: Tue, 16 Jan 2018 08:30:10 +0100 From: Jo?o Henriques To: gmx-us...@gromacs.org Subject: Re: [gmx-users] -inter command Message-ID:

Re: [gmx-users] interaction force between Mg and Oxygens of phosphate, in CHARM36 force field

On 1/20/18 2:42 AM, Sajad Ahrari wrote: Hello Dears, I am using CHARM-36.ff for my simulation. I have Mg ions and ATP as hetero-atoms in my system (the Mg-ATP complex). I am trying to know about the amount of interaction force between Mg ions and phosphates of ATP that is already set in

Re: [gmx-users] disulfide bond missing even with -ss

On 1/21/18 10:29 AM, MD wrote: I modified the specbond.dat and change the cutoff to be 2.04A, still nothing... Please don't spam the list with minute-by-minute updates. Provide your pdb2gmx command, full screen output, and whatever evidence you have that the bond wasn't formed. The

Re: [gmx-users] disulfide bond missing even with -ss

I modified the specbond.dat and change the cutoff to be 2.04A, still nothing... On Sun, Jan 21, 2018 at 10:23 AM, MD wrote: > I have also tried renaming my two CYS to be CYS2 but no luck either. > > On Sun, Jan 21, 2018 at 10:22 AM, MD wrote: > >> gromacs

Re: [gmx-users] disulfide bond missing even with -ss

I have also tried renaming my two CYS to be CYS2 but no luck either. On Sun, Jan 21, 2018 at 10:22 AM, MD wrote: > gromacs did ask me to confirm linking the two cys before the run, but I > didn't see any log saying the bond is formed. > > On Sun, Jan 21, 2018 at 10:19 AM, MD

Re: [gmx-users] disulfide bond missing even with -ss

gromacs did ask me to confirm linking the two cys before the run, but I didn't see any log saying the bond is formed. On Sun, Jan 21, 2018 at 10:19 AM, MD wrote: > Hi Gromacs folks, > I realized I kept losing disulfide bond after gmx. The length is 2.01A but > I did use -ss

[gmx-users] disulfide bond missing even with -ss

Hi Gromacs folks, I realized I kept losing disulfide bond after gmx. The length is 2.01A but I did use -ss when pdb2gmx. Any thoughts? Thanks, Ming -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't

[gmx-users] gmx dipole and gmx potential

Hİ all I am newbie and GROMACS, I did some dipole moment and electric potential calculation for water solutions. I want to understand gmx dipole and gmx potential algorithm.I read GROMACS manual 8.5.4 and 8.5.3 but I can not understand about gmx dipole algorithm, so I need information about gmx

Re: [gmx-users] (no subject)

> You need some ions to neutralise the system for long range electrostatics to work. This mostly applies to PME. However, because PME is basically *de facto* nowadays, it will most likely apply in most situations. However, I recently learned that PME can also be run with a non-neutral system, as