[gmx-users] Problem on pbc atom

Dear gromacs users, I am using following pull code in md simulation for pulling a ligand across the plasma membrane model. My size box is 8.52807 8.52807 14.0. And the pull distance is less than one-half the length of the box vector along.pull distance is 6 nm. when I execute this

[gmx-users] Umbrella sampling on lipid bilayer

Dear gromacs users, Sorry for repeating my question. I didn't receive any email so I couldn't reply and I missed them. I am using following pull code in md simulation for pulling a ligand across the plasma membrane model. Ligand passes through the membrane,but along simulation, the size of

[gmx-users] (no subject)

Dear gromacs users, Sorry for repeating my question. I didn't receive any email so I couldn't reply and I missed them. I am using following pull code in md simulation for pulling a ligand across the plasma membrane model. Ligand passes through the membrane,but along simulation, the size of

Re: [gmx-users] Umbrella sampling on lipid bilayer

the membrane . Thank you . Regards Mahsa [image: Mailtrack] <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality5;> Sender notified by Mailtrack <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality5;> 09/25/19, 03:36:2

[gmx-users] Umbrella sampling on lipid bilayer

. Regards Mahsa. Does it do that without using the pull code, i.e. just performing NPT simulation? What is physically happening? Sounds like the bilayer is unstable. What forcefield is this? Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences

[gmx-users] Umbrella sampling on lipid bilayer

Dear gromacs users, I am using following pull code in md simulation for pulling a ligand across the plasma membrane model. Ligand passes through the membrane,but along simulation, the size of axis z increases. My size box is 8.52807 8.52807 14.0. And the pull distance is less than one-half

Re: [gmx-users] Some suggestions about the gmx current tool

Hi Mark, Thank you for your reply! I opened a new issue with this information in the link you mentioned. Best regards, Mahsa On Wed, Jun 12, 2019 at 10:26 PM Mark Abraham wrote: > Hi Mahsa, > > Thanks very much for your feedback. Those look like useful changes to the > code. Ca

Re: [gmx-users] Some suggestions about the gmx current tool

Hi again, Something went wrong with the equations which I tried to show. So for the first equation please see eq. 9 in this paper: https://aip.scitation.org/doi/10.1063/1.2868752 and the second missing formula is: 1 / 6*V*K_B*T = 7.20677e-12 Best regards, Mahsa On Wed, Jun 12, 2019 at 3:12

[gmx-users] Some suggestions about the gmx current tool

the reported sigma value in the output of dsp.xvg should be multiplied by 10^-12 manually. It took sometime for me to understand what is going on in the output :-) Please correct me if I'm wrong or missed something in these comments. Best regards, Mahsa -- Gromacs Users mailing list * Please

[gmx-users] (no subject)

mahs.rez...@mail.sbu.ac.ir -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit

[gmx-users] Contact autocorrelation function in Gromacs

lar question: https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2011-June/062181.html Does this means that I should consider the second column of y values in the contac_ac.xvg file instead of the first one? Best regards, Mahsa -- Gromacs Users mailing list * Please search the archive at h

Re: [gmx-users] Fwd: Probability of number of atomic contacts

shell coordination number for specific groups during the simulation time. Is this correct? because the coordination number from gmx rdf gives the average number of particles within a distance r. Best regards, Mahsa On Fri, Mar 1, 2019 at 12:11 PM Mahsa wrote: > Hi Mark, > > Thank you

Re: [gmx-users] Fwd: Probability of number of atomic contacts

of particles within a distance r. Best regards, Mahsa On Fri, Mar 1, 2019 at 5:04 AM Mark Abraham wrote: > Hi, > > Which GROMACS tools documentation did you check to see whether it can be > done already? :-) I don't know the answer, but that's where to start! > > Mark > &g

Re: [gmx-users] Fwd: Probability of number of atomic contacts

Thank you very much for your comments! How would it be possible to get probability vs. number of contacts or probability vs coordination number averaged across the simulations? Can it be done directly with Gromacs tools or I need some scripts for that? Best regards, Mahsa On Thu, Feb 28, 2019

[gmx-users] Fwd: Probability of number of atomic contacts

Hi Justin, Could you please comment on my questions in the previous post? Best regards, Mahsa -- Forwarded message - From: Mahsa Date: Sun, Feb 17, 2019 at 2:36 PM Subject: Re: [gmx-users] Probability of number of atomic contacts To: Thank you very much, Justin! I tried

Re: [gmx-users] Probability of number of atomic contacts

the same approach to get the distribution of coordination number for the first coordination shell of ions and special atoms of the polymers? Best regards, Mahsa On Sun, Feb 17, 2019 at 1:39 PM Justin Lemkul wrote: > > > On 2/17/19 7:21 AM, Mahsa wrote: > > Dear Gromacs users,

[gmx-users] Probability of number of atomic contacts

and then the polymer group. The generated file numcont.xvg which is more related to what I am looking for, gives number of contacts vs time. How can I get the information which I look for from this analysis? Best regards, Mahsa -- Gromacs Users mailing list * Please search the archive at http

Re: [gmx-users] RDF calculations for certain atoms in a polymer

Thank you for your reply! Best regards, Mahsa On Mon, Aug 13, 2018 at 2:47 PM, Mark Abraham wrote: > Hi, > > You need a composite selection, eg of an atomtype and residue type or > molecule type. Make a selection of the atomtype and another of whatever > seems suitable, a

Re: [gmx-users] RDF calculations for certain atoms in a polymer

Dear Mark, Could you please comment on my previous question? I would really appreciate it. Best regards, Mahsa On Sat, Aug 11, 2018 at 12:52 PM, Mahsa wrote: > Hi Mark, > > Thank you for your reply! > > I tried gmx make_ndx -f topol.tpr -o index.ndx before and then s

Re: [gmx-users] RDF calculations for certain atoms in a polymer

. Then with this approach I get both O types in a group while I should have them separately. Could you help me with this problem? I don't know how to specify this one for the RDF calculations. Best regards, Mahsa On Sat, Aug 11, 2018 at 12:22 PM, Mark Abraham wrote: > Hi, > > Making a

[gmx-users] RDF calculations for certain atoms in a polymer

specify the O of the side chain in the index file to tell it apart from the other O atoms? Besides there are around 500 of this atom in the system so changing something manually is not a good option either. Best regards, Mahsa -- Gromacs Users mailing list * Please search the archive at http

Re: [gmx-users] Positive potential energy

Hi, Thanks for your help, Justin! Regards, Mahsa On Sun, Feb 25, 2018 at 5:53 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 2/25/18 10:15 AM, Mahsa wrote: > >> Dear Justin, >> >> Thank you for your reply! >> >> In general, is it a g

Re: [gmx-users] Positive potential energy

and ions, should I use pbc or not and which of the mdp files in my first post is correct? Regards, Mahsa On Sun, Feb 25, 2018 at 3:39 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 2/25/18 9:26 AM, Mahsa wrote: > >> Dear Mark, >> >> Thank you for your reply. H

Re: [gmx-users] Positive potential energy

mean that the steep integrator is not good to do energy minimization for this type of simulation? Would you please help me to fix these problems? Regards, Mahsa On Sat, Feb 24, 2018 at 8:54 AM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > Hi, > > Even if there are minima on the surfa

[gmx-users] Positive potential energy

in the simulation which I'm not aware of? Regards, Mahsa -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit

Re: [gmx-users] Calculate RDF within a certain distance from atom

Hi, I think the selection keywords in the manual are helpful: http://manual.gromacs.org/documentation/5.1/onlinehelp/selections.html#selection-examples /Mahsa On Tue, Feb 20, 2018 at 5:53 PM, Dilip H N <cy16f01.di...@nitk.edu.in> wrote: > Hello, > How to get RDF within a cert

Re: [gmx-users] Changes in the simulation box after the production run

Thank you very much for the links! Best regards, Mahsa On Mon, Sep 18, 2017 at 1:30 AM, Dallas Warren <dallas.war...@monash.edu> wrote: > These two images will help you see what is going on: > > https://twitter.com/dr_dbw/status/909559339366572032 - shows a > molecule that app

Re: [gmx-users] Changes in the simulation box after the production run

Thank you for you quick reply, Justin and Dallas! Very good point! Best regards, Mahsa On Mon, Sep 18, 2017 at 1:00 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 9/17/17 6:57 PM, Mahsa E wrote: > >> Could you please see the link below for the input and

Re: [gmx-users] Changes in the simulation box after the production run

with another polymer, I didn't see this difference in the systems after the production run, so I'm wondering if this is related to the stability of the system? Best regards, Mahsa On Mon, Sep 18, 2017 at 12:10 AM, Dallas Warren <dallas.war...@monash.edu> wrote: > Because that is how the syste

[gmx-users] Changes in the simulation box after the production run

ing lincs_warnangle = 30; [degrees] maximum angle that a bond can rotate before LINCS will complain Best regards, Mahsa -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? R

Re: [gmx-users] Generating topology file for a long polymer chain

Thank you for your help! Best regards, Mahsa On Mon, Aug 7, 2017 at 4:35 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 8/6/17 8:35 PM, Mahsa E wrote: > >> Hello Justin, >> >> Thank you so much for your reply! >> >> I followed what you

Re: [gmx-users] Generating topology file for a long polymer chain

to generate the .itp file for a longer chain of polymer (like 25 units)? Your kind help on this is very much appreciated. Best regards, Mahsa On Sun, Aug 6, 2017 at 2:34 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 8/5/17 8:12 AM, Mahsa E wrote: > >> Dear gmx-users, &g

[gmx-users] Generating topology file for a long polymer chain

a conformation with different angles and dihedrals than in the monomer. In general, how can I use the topology file of a monomer for the longer chain of a polymer? Could you please advise me? Best regards, Mahsa -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support

[gmx-users] Generating topology file for a long polymer chain

a conformation with different angles and dihedrals than in the monomer. In general, how can I use the topology file of a monomer for the longer chain of a polymer ? Could you please advise me? Best regards, Mahsa -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org