[gmx-users] Umbrella Sampling with water molecules flying away from the reference point

Dear GROMACS users, Currently I am experiencing a problem. At the moment I am trying to do a umbrella sampling with water going through a porous material. I have generate the configuration based on CV direction (1,1,1). However when I watch the movie back for individual simulation. I see the

Re: [gmx-users] Umbrella Sampling - good histogram but no result in profile

lem remains that something about how you sampled didn't meet the expectations of gmx wham. Mark On Wed, Mar 14, 2018, 15:45 Ben Tam <btam...@hotmail.co.uk> wrote: > Dear all, > > I have a rather strange problem. Currently I am trying to get a PMF of a > water molecule throug

[gmx-users] Umbrella Sampling - good histogram but no result in profile

Dear all, I have a rather strange problem. Currently I am trying to get a PMF of a water molecule through a hydrophobic materials. At the end of using "gmx wham", I get a rather good histogram and it cover the whole range of the system. However at the making profile.xvg. I get the answer "nan"

Re: [gmx-users] Using xy periodic boundary and 3dc Ewald summation

ail_source=link_campaign=sig-email_content=webmail> Virus-free. www.avg.com<http://www.avg.com> <http://www.avg.com/email-signature?utm_medium=email_source=link_campaign=sig-email_content=webmail> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> On Mon, Feb 5, 2018 at 11:57 AM, Ben Tam &l

[gmx-users] Using xy periodic boundary and 3dc Ewald summation

Dear GROMACS user, Currently I am simulating a Metal Organic Frameworks membrane, in which I have applied vacuum space at z direction (3 times of the current non-vacuum system). Following the instruction on GROMACS, I have set the pbc = xy and ewald-geometry = 3dc. So here is my first

Re: [gmx-users] umbrella sampling

behalf of Justin Lemkul <jalem...@vt.edu> Sent: Tuesday, July 11, 2017 18:07 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] umbrella sampling On 7/11/17 12:53 PM, Ben Tam wrote: > Hi Andre, > > > Thanks for your answer. Actually I should clarify it is > metal-organic-framework

Re: [gmx-users] umbrella sampling

kely a trial and error procedure until you fine-tune the forces along the profile. best Andre On Tue, Jul 11, 2017 at 1:09 PM, Ben Tam <btam...@hotmail.co.uk> wrote: > Dear All, > > I am doing umbrella sampling for a water molecules moving inside a crystal > structure, however I am r

[gmx-users] umbrella sampling

Dear All, I am doing umbrella sampling for a water molecules moving inside a crystal structure, however I am running into a problem on the output file with profile.xvg all value showing “nan”. This error has occurred when I reduce the slide width from 0.2 nm to 0.1 nm. I have used the exact

Re: [gmx-users] Problems with large molecule simulation

Dear gromacs user, I am trying to simulate a large system, but I ran into some fundamental problems. For example in the .gro file, the name of the atoms merge with the number count: 2MOL C2 9998 3.987 2.259 6.276 2MOL C5 3.987 2.061 6.079 2MOL C11

[gmx-users] Membrane simulation error

Dear gromacs user, I am doing a membrane simulation, however I have this error message pop up when I do energy minimisation: Program gmx mdrun, VERSION 5.1.1 Source code file: /dev/shm/tmp.PwtfSrm0uJ/gromacs-5.1.1/src/gromacs/mdlib/nbnxn_search.c, line: 734 Software inconsistency error:

Re: [gmx-users] X2top usage

...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of David van der Spoel <sp...@xray.bmc.uu.se> Sent: 07 September 2016 14:33 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] X2top usage On 07/09/16 13:48, Ben Tam wrote: > Dear gromacs user. &

[gmx-users] X2top usage

Dear gromacs user. I am using gmx x2top to write a rough connectivity map for the crystal structure that I am using. In the conf.gro file, there are many ions with no bond to any other molecules. How do I specify that on .n2t file? Because when I do specify it with: Mg Mg 0.000

[gmx-users] Tabulation table error

Dear gromacs user, I am trying to learn how to use tabulation table because I need a mix of Lennard Jones and Buckingham interaction. The tabulated simulation ran for a few ps before crashing with this error: A list of missing interactions: Angle of730 missing 1

Re: [gmx-users] Problem with binding energy

: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Justin Lemkul <jalem...@vt.edu> Sent: 18 August 2016 13:21 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Problem with binding energy On 8/18/16 8:13 AM, Ben Tam wrote

Re: [gmx-users] Problem with binding energy

with binding energy Hi Ben, My understanding of what you've done is that you have calculated a binding enthalpy for the water at a specific, non-biological temperature, and not a Gibbs free energy that you would expect from experiment... Billy On 18 August 2016 at 21:34, Ben Tam <btam..

[gmx-users] Problem with binding energy

Dear all, I have a problem with calculation with binding energy with using gromacs. My calculation is the binding of solvent onto a crystal. The steps I took to calculate binding energy is like this: 1) Energy minimised my crystal system with the solvent. 2) Calculated the energy of the

Re: [gmx-users] Reading Force field

ts how, make a .tpr and then use mdrun -rerun passing a file with one or more configurations where you want to find out energy or force. Mark On Mon, Jul 18, 2016 at 3:35 PM Ben Tam <btam...@hotmail.co.uk> wrote: > Dear Gromacs User, > > > I am trying to do a bit of debugging on t

Re: [gmx-users] Problem with Group and Verlet cut -off scheme

Jul 2016 16:55 Ben Tam <btam...@hotmail.co.uk> wrote: > Hi Justin, > > > This is what I got from the log file: > > > Initializing Domain Decomposition on 6 ranks > Dynamic load balancing: auto > Will sort the charge groups at every domain (re)decomposition &

Re: [gmx-users] Problem with Group and Verlet cut -off scheme

ers-boun...@maillist.sys.kth.se> on behalf of Justin Lemkul <jalem...@vt.edu> Sent: 08 July 2016 17:17 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Problem with Group and Verlet cut -off scheme On 7/8/16 12:05 PM, Ben Tam wrote: > Dear all, > > > My systems si

Re: [gmx-users] Problem with Group and Verlet cut -off scheme

-off scheme On 7/8/16 10:54 AM, Ben Tam wrote: > Hi Justin, > > > This is what I got from the log file: > > > Initializing Domain Decomposition on 6 ranks > Dynamic load balancing: auto > Will sort the charge groups at every domain (re)decomposition > Initial maximum in

Re: [gmx-users] Problem with Group and Verlet cut -off scheme

ct: Re: [gmx-users] Problem with Group and Verlet cut -off scheme On 7/8/16 10:20 AM, Ben Tam wrote: > Hi Mark, > > > It shouldn't, what I am simulated is a crystal structure and my tabulated > forcefield is only up to 3nm. Do you think the problem is there? To avoid the &

Re: [gmx-users] Problem with Group and Verlet cut -off scheme

-off scheme Hi, Why does your topology have an interaction between atoms that are ~6 nm apart? Mark On Fri, Jul 8, 2016 at 12:37 PM Ben Tam <btam...@hotmail.co.uk> wrote: > Hi Mark, > > > Thank you for your reply and your suggestion. Now I get it working, I have > another

Re: [gmx-users] Problem with Group and Verlet cut -off scheme

braham <mark.j.abra...@gmail.com> Sent: 07 July 2016 15:07 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Problem with Group and Verlet cut -off scheme Hi, On Thu, Jul 7, 2016 at 3:44 PM Ben Tam <btam...@hotmail.co.uk> wrote: > Dear Gromacs users, > > > Thank you ve

[gmx-users] Problem with Group and Verlet cut -off scheme

Dear Gromacs users, Thank you very reading. I am trying to run a simulation that requires me to use lennard jones and buckingham potential mix, thus I have to make my own tabulated table .xvg list. However here is my problem, because Verlet does not support tabulated table so I have to use

Re: [gmx-users] Problem with running crystal simulation

> Is your topology correctly connecting the atoms through the box wall so you > have a periodic molecule? Have you set "periodic_molecules = yes" in your > MDP files? > > Cheers, > -- > Elton Carvalho > > On Mon, Nov 23, 2015 at 3:58 PM, Ben Tam <btam...@hotmail.co.uk>

[gmx-users] Problem with running crystal simulation

Dear GROMACS user, I have a problem here when I am trying to run a crystal simulation, this is the warning I am getting from the error file: Warning: Only triclinic boxes with the first vector parallel to the x-axis and the second vector in the xy-plane are supported. Box (3x3):

Re: [gmx-users] Getting a crystal topology file from pdb2gmx

; From: jalem...@vt.edu > Date: Wed, 11 Nov 2015 11:19:46 -0500 > Subject: Re: [gmx-users] Getting a crystal topology file from pdb2gmx > > > > On 11/11/15 11:05 AM, Ben Tam wrote: > > Hi Justin, > > > > I am using Gaussian with basis set 6-31G* and LanL2DZ to c

[gmx-users] Getting a crystal topology file from pdb2gmx

Dear Gromacs users and Developer, I am trying to run a simulation for a metal organic frameworks (MOFs), it is a crystallise periodic structure. The original file is in .cif format, however using material studio I converted it to .pdb file. Now I am stuck on converting .pdb file to a topology

Re: [gmx-users] Getting a crystal topology file from pdb2gmx

opology file from pdb2gmx > > > > On 11/11/15 10:37 AM, Ben Tam wrote: > > Hi Micholas, > > I am using CHARMM27. > > And, out of curiosity, what is the source of your Zr parameters? > > -Justin > > > Ben > > > >> From: smit...@ornl.gov &

Re: [gmx-users] Getting a crystal topology file from pdb2gmx

gmx-users-boun...@maillist.sys.kth.se > <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Ben Tam > <btam...@hotmail.co.uk> > Sent: Wednesday, November 11, 2015 10:10 AM > To: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: [gmx-users] Getting a crysta