Re: [gmx-users] tutorial problem

Hi, Your working directory is the one in which you are doing your work. You are making a copy of the normal force field folder, so that next time you use it, you know it is unchanged from what GROMACS provides. Having made the copy, edit the files in the copy. Mark On Sun, Jul 22, 2018, 09:49

[gmx-users] tutorial problem

dear all I am a new user,I was doing this tutorial(http://www.mdtutorials.com/gmx/membrane_protein/index.html) it said {To use the parameters in lipid.itp, we will have to make some changes to our pre-packaged GROMOS96 53A6 force field files (in $GMXLIB/gromos53a6.ff). Make a copy of

[gmx-users] Tutorial for calculating diffusion from umbrella sampling

Dear Experts,Is there any tutorial available online for understanding procedure to calculate diffusion coefficient from umbrella sampled force and position trajectory data. The formula for diffusion is given as D()=variance(z)/tau. Numerator is variance of z (or

[gmx-users] Tutorial

Hi, is there a tutorial for importing fully charged non-peptid topologies for the AMBER FF ISBN type to GMX somewhere ? Thanks Sergio Manzetti Fjordforsk AS Midtun 6894 VangsnesNorge Org.nr. 911 659 654 Tlf: +47 57695621Økolab | Nanofactory |

Re: [gmx-users] Tutorial #3 : Umbrella Sampling (By Justin Lemkul)

On 6/21/16 1:49 AM, amitbe...@chemeng.iisc.ernet.in wrote: Hello, The summary_distances.dat file contains only one column ( the column for COM is missing). I am using GROMACS 5.1.2. How to solve this issue. I feel like I've answered this same exact question several times in the last week.

[gmx-users] Tutorial #3 : Umbrella Sampling (By Justin Lemkul)

Hello, The summary_distances.dat file contains only one column ( the column for COM is missing). I am using GROMACS 5.1.2. How to solve this issue. Regards, Amit Behera Research Scholar, Dept. of Chemical Engineering, IISc -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Tutorial 2: KALP-15 in DPPC

On 6/20/16 4:08 PM, Kyle Titus-Glover wrote: Sure, I can gather up the files and send them in a compressed folder to you school email if that's ok. Yes. The sequence of commands (in an executable script) is also essential. A dump of files is only a small part of the equation. -Justin

Re: [gmx-users] Tutorial 2: KALP-15 in DPPC

Sure, I can gather up the files and send them in a compressed folder to you school email if that's ok. Kyle Titus-Glover On Mon, Jun 20, 2016 at 3:45 PM, Justin Lemkul wrote: > > > On 6/20/16 3:11 PM, Kyle Titus-Glover wrote: > >> However, I did look into system_shrink1.gro

Re: [gmx-users] Tutorial 2: KALP-15 in DPPC

On 6/20/16 3:11 PM, Kyle Titus-Glover wrote: However, I did look into system_shrink1.gro and saw that the file was missing the peptides and that 2 DPPC molecules still remained undeleted. Should I manually correct the coordinate file? No, you should correct whatever it is that you're doing

Re: [gmx-users] Tutorial 2: KALP-15 in DPPC

However, I did look into system_shrink1.gro and saw that the file was missing the peptides and that 2 DPPC molecules still remained undeleted. Should I manually correct the coordinate file? On Mon, Jun 20, 2016 at 3:09 PM, Kyle Titus-Glover wrote: > I tried restarting the whole

Re: [gmx-users] Tutorial 2: KALP-15 in DPPC

I tried restarting the whole process to go back and carefully look and make sure that nothing was spelled right. Bu I still get the same error. On Mon, Jun 20, 2016 at 2:36 PM, Justin Lemkul wrote: > > > On 6/20/16 2:32 PM, Kyle Titus-Glover wrote: > >> Hey everyone, >> >>

Re: [gmx-users] Tutorial 2: KALP-15 in DPPC

On 6/20/16 2:32 PM, Kyle Titus-Glover wrote: Hey everyone, I've been working on the Justin Lemkul's 2nd tutorial and just can't seem to get past 2. packing the lipids around the protein and 3. solvating with water. The follow the instructions step by step but for some reason as I try to run

[gmx-users] Tutorial 2: KALP-15 in DPPC

Hey everyone, I've been working on the Justin Lemkul's 2nd tutorial and just can't seem to get past 2. packing the lipids around the protein and 3. solvating with water. The follow the instructions step by step but for some reason as I try to run EM with gmx grompp -f minim.mdp -c

[gmx-users] Tutorial 2: KALP-15 in DPPC

Hey everyone, I've been working on the Justin Lemkul's 2nd tutorial and just can't seem to get past 2. packing the lipids around the protein and 3. solvating with water. The follow the instructions step by step but for some reason as I try to run EM with gmx grompp -f minim.mdp -c

Re: [gmx-users] tutorial for "dual" alchemical transformation in gromacs?

your two dummy types appear to be identical > you can define just one. > > Cheers, > Hannes. > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Sebast

Re: [gmx-users] tutorial for "dual" alchemical transformation in gromacs?

s lambda=1 corresponds to "typeB", so my > >>> transformation is "XX" -> "Na+", "Cl-" -> "XX" > >>> > >>> Thanks a bunch, > >>> Sebastian > >>> > >>> > >>> &

Re: [gmx-users] tutorial for "dual" alchemical transformation in gromacs?

>>> >>> On 30.11.2015 17:30, hannes.loeff...@stfc.ac.uk wrote: >>>> Dear Sebastian, >>>> >>>> I have some trouble reading your top file in my web browser but I >>>> think your transformations are IPX->Na+, IMX->Cl-. So you would >>>

Re: [gmx-users] tutorial for "dual" alchemical transformation in gromacs?

eading your top file in my web browser but I > > > think your transformations are IPX->Na+, IMX->Cl-. So you would > > > have to reverse the columns for the first atom. As your two dummy > > > types appear to be identical you can define just one. > > > &g

Re: [gmx-users] tutorial for "dual" alchemical transformation in gromacs?

efine just one. > > > > Cheers, > > Hannes. > > > > ________ > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > > [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of > > Sebastian Stolzenberg [s.sto

Re: [gmx-users] tutorial for "dual" alchemical transformation in gromacs?

anual > describes how to set up the A and the B state of a molecule. > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Sebastian > Stolzenberg [s.stolzenb.

Re: [gmx-users] tutorial for "dual" alchemical transformation in gromacs?

le. > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Sebastian > Stolzenberg [s.stolzenb...@fu-berlin.de] > Sent: 29 November 2015 13:11 > To: gromacs.org_gmx-user

Re: [gmx-users] tutorial umbrella sampling

Thanks, that did the trick! Now everything works fine. Am 29.11.2015 um 12:00 schrieb gromacs.org_gmx-users-requ...@maillist.sys.kth.se: On 11/27/15 5:36 PM, Matthias Kiesel wrote: Hi All, I am currently doing the umbrella sampling tutorial by Justin Lemkul, but i have a problem with

[gmx-users] tutorial for "dual" alchemical transformation in gromacs?

Dear Gromacs experts, I am looking for a Gromacs tutorial to perform a "dual" alchemical transformation in a water box, i.e. a mutation or any other alchemical transformation, in which: the nonbonded interactions between the environment and a molecule A disappear as lambda goes from 0 to 1,

Re: [gmx-users] tutorial for "dual" alchemical transformation in gromacs?

er 2015 13:11 To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] tutorial for "dual" alchemical transformation in gromacs? Dear Gromacs experts, I am looking for a Gromacs tutorial to perform a "dual" alchemical transformation in a water box, i.e. a mu

Re: [gmx-users] tutorial umbrella sampling

On 11/27/15 5:36 PM, Matthias Kiesel wrote: Hi All, I am currently doing the umbrella sampling tutorial by Justin Lemkul, but i have a problem with creating the right configurations for the umbrella sampling run. After running the first pull simulation and the given perl script the com

[gmx-users] tutorial umbrella sampling

Hi All, I am currently doing the umbrella sampling tutorial by Justin Lemkul, but i have a problem with creating the right configurations for the umbrella sampling run. After running the first pull simulation and the given perl script the com distances don´t go from 0.5nm to 5nm, instead

[gmx-users] tutorial

Dear all, I am trying to follow the tutorial: http://nmr.chem.uu.nl/~adrien/course/molmod/analysis2.html Part: ANALYSIS OF DYNAMICS AND TIME-AVERAGED PROPERTIES In the command: trjconv -f traj_helix.xtc -o traj_helix_10-50ns.xtc -n _peptide_index.ndx -pbc nojump -dt 100 -b 1 what is

[gmx-users] tutorial

Dear all, I am trying to follow the tutorial: http://nmr.chem.uu.nl/~adrien/course/molmod/analysis2.html Part: ANALYSIS OF DYNAMICS AND TIME-AVERAGED PROPERTIES In the command: trjconv -f traj_helix.xtc -o traj_helix_10-50ns.xtc -n _peptide_index.ndx -pbc nojump -dt 100 -b 1 what is

Re: [gmx-users] tutorial

Hi Urszula, I suspect it's a naming inconsistency or the tutorial got garbled. Maybe you can contact Adrien Melquiond about this. Cheers, Tsjerk On Thu, Oct 15, 2015 at 1:02 PM, Urszula Uciechowska < urszula.uciechow...@biotech.ug.edu.pl> wrote: > Dear all, > > I am trying to follow the

Re: [gmx-users] Tutorial site down

Dear Justin, I hope all thing will be on its road soon :) Tuong Vy 2015-06-02 23:12 GMT+09:00 Justin Lemkul jalem...@vt.edu: All, Yesterday we experienced a hardware failure on the server that hosts my GROMACS tutorials. We are aware of the issue and are going to be setting up a new

[gmx-users] Tutorial site down

All, Yesterday we experienced a hardware failure on the server that hosts my GROMACS tutorials. We are aware of the issue and are going to be setting up a new server. The tutorials may end up on this new server or another; I haven't decided yet. For the next few days, the tutorials will

Re: [gmx-users] Tutorial For Installing Gromacs on window

On 3/19/15 12:30 AM, Rajneet kaur Saini wrote: Greetings, I want to install gromacs on window 7. but i don't know the exact procedure.could you please explain me the procedure to install gromacs on window. Thanking you in anticipation

[gmx-users] Tutorial For Installing Gromacs on window

Greetings, I want to install gromacs on window 7. but i don't know the exact procedure.could you please explain me the procedure to install gromacs on window. Thanking you in anticipation -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Tutorial updates

Hi Justin, Do you plan to keep the Gromacs 4.x versions of your tutorials (which by the way are excellent) around for a little longer as well? From my experience It will still take quite some time until Gromacs 5 is available on most Clusters and Linux-package repositories, whereas the Gromacs 4

Re: [gmx-users] Tutorial updates

On 7/9/14, 2:40 PM, Oliver Stueker wrote: Hi Justin, Do you plan to keep the Gromacs 4.x versions of your tutorials (which by the way are excellent) around for a little longer as well? From my experience It will still take quite some time until Gromacs 5 is available on most Clusters and