[gmx-users] COM removal note

Hi, I am running some MD simulation using position restraints and turning-off centre of mass removal (comm-mode = None in the .mdp file). However, GROMACS 2020 still tell me with a note that 'removing center of mass motion in the presence of position restraints might cause artifacts'. So, is

Re: [gmx-users] com motion and position restraints may cause artifacts

To: gmx-us...@gromacs.org Subject: Re: [gmx-users] com motion and position restraints may cause artifacts The ambiguity in the gromacs 2020 note made me concerned, as it was not clear to me whether my system (DNA+small molecule) fills in the category where artifacts are caused. The gromacs note

Re: [gmx-users] com motion and position restraints may cause artifacts

To: gmx-us...@gromacs.org Subject: Re: [gmx-users] com motion and position restraints may cause artifacts The ambiguity in the gromacs 2020 note made me concerned, as it was not clear to me whether my system (DNA+small molecule) fills in the category where artifacts are caused. The gromacs note could have

Re: [gmx-users] com motion and position restraints may cause artifacts

The ambiguity in the gromacs 2020 note made me concerned, as it was not clear to me whether my system (DNA+small molecule) fills in the category where artifacts are caused. The gromacs note could have been a bit more helpful by referencing specific publications so that we can educate

Re: [gmx-users] com motion and position restraints may cause artifacts

On 1/16/20 5:17 AM, Alessandra Villa wrote: Hi, On Mon, Jan 13, 2020 at 3:36 PM Christos Deligkaris wrote: dear all, I installed gromacs 2020 and I now get the following message during equilibration: NOTE 1 [file nvt.mdp]: Removing center of mass motion in the presence of position

Re: [gmx-users] com motion and position restraints may cause artifacts

Hi, On Mon, Jan 13, 2020 at 3:36 PM Christos Deligkaris wrote: > dear all, > > I installed gromacs 2020 and I now get the following message during > equilibration: > > NOTE 1 [file nvt.mdp]: > > Removing center of mass motion in the presence of position > restraints might cause artifacts > >

[gmx-users] com motion and position restraints may cause artifacts

dear all, I installed gromacs 2020 and I now get the following message during equilibration: NOTE 1 [file nvt.mdp]: Removing center of mass motion in the presence of position restraints might cause artifacts I do not recall seeing this with gromacs 2018. In which cases are artifacts

Re: [gmx-users] COM

; > > > > > > > De: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > > > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> em nome de laura > O. < > > > laura.o.vendr...@gmail.com> > > >

Re: [gmx-users] COM

ura.o.vendr...@gmail.com> > > Enviado: 22 de janeiro de 2019 17:31 > > Para: gromacs.org_gmx-users@maillist.sys.kth.se > > Assunto: [gmx-users] COM > > > > Dear Users. > > > > I'm trying to calculate the center of mass distance between > cyc

Re: [gmx-users] COM

ura O. < > laura.o.vendr...@gmail.com> > Enviado: 22 de janeiro de 2019 17:31 > Para: gromacs.org_gmx-users@maillist.sys.kth.se > Assunto: [gmx-users] COM > > Dear Users. > > I'm trying to calculate the center of mass distance between cyclodextrine ( > HAGD) and a biolo

Re: [gmx-users] COM

cs.org_gmx-users@maillist.sys.kth.se Assunto: [gmx-users] COM Dear Users. I'm trying to calculate the center of mass distance between cyclodextrine ( HAGD) and a biological molecule (MTX). I've searched on gromacs documentation in gmx distance I use command line: gmx distance -f fixv1

Re: [gmx-users] COM

Hi, Thanks but I already tried without the double quotation marks but the result was the same. - Cannot match 'group "HAGD"', because no such index group can be found.

Re: [gmx-users] COM

Em ter, 22 de jan de 2019 às 16:01, Quyen VuVan escreveu: > Hi, > I don't think you need a double quote in your select HAGD > > On Tue, Jan 22, 2019 at 6:32 PM laura O. > wrote: > > > Dear Users. > > > > I'm trying to calculate the center of mass distance between > cyclodextrine ( > > HAGD) and

Re: [gmx-users] COM

Hi, I don't think you need a double quote in your select HAGD On Tue, Jan 22, 2019 at 6:32 PM laura O. wrote: > Dear Users. > > I'm trying to calculate the center of mass distance between cyclodextrine ( > HAGD) and a biological molecule (MTX). > I've searched on gromacs documentation in gmx

[gmx-users] COM

Dear Users. I'm trying to calculate the center of mass distance between cyclodextrine ( HAGD) and a biological molecule (MTX). I've searched on gromacs documentation in gmx distance I use command line: gmx distance -f fixv1out.xtc -s bcd_mtx_solv_min.tpr -n fix.ndx -oav cmtransv1.xvg -select

[gmx-users] COM

Dear Users. I'm trying to calculate the center of mass distance between cyclodextrine ( HAGD) and a biological molecule (MTX). I've searched on gromacs documentation in gmx distance I use command line: gmx distance -f fixv1out.xtc -s bcd_mtx_solv_min.tpr -n fix.ndx -oav cmtransv1.xvg -select

[gmx-users] COM pulling: Reference position in space

Dear GMX community, I read on manual of gromacs that the reference group in pulling code can be defined by absolute position in space. How can I change my setup for that purpose, for example the coordinate of reference point X0 Y0 Z0 ; Pull code pull= yes pull_ncoords

[gmx-users] COM-pulling

Hello, I tried to do COM-pulling simulation (using Gromacs 5 .0.4) to pull a molecule away from sodium ion that is bound to acidic site of protein. My reference group is protein backbone. I do that in presence of solvent. The main problem is that my pulled group is not pulled in linear

[gmx-users] COM-RDF calculation

Hello, I am trying to calculate the center of mass (COM) rdfs for methanol molecules. I have noticed that in gromacs 2016 there is neither -com nor -rdf option for gmx rdf. I have used the following instead: gmx rdf -f traj.trr -n index.ndx -s topol.tpr -pbc -seltype whole_mol_com -selrpos

[gmx-users] COM pulling with gromacs 5.0.x

Hi, I have a problem to use the COM pulling with the Gromacs version 5.0.X or 5.1.x. We are working on membrane simulations (using Coarse-grained Martini Force Field). From a big membrane system with POPC lipid, we selected a small patch of lipids in the center (POPX) and pulled this patch in z

Re: [gmx-users] COM pulling

On 8/16/17 3:40 AM, Naba wrote: Dear users, Please let me know whether it is feasible and relevant or not if I use COM pulling for mechanical unfolding of proteins. More specifically, whether I can define the two group within the same molecule !! You can define groups of any atoms, and you

[gmx-users] COM pulling

Dear users, Please let me know whether it is feasible and relevant or not if I use COM pulling for mechanical unfolding of proteins. More specifically, whether I can define the two group within the same molecule !! Sorry for the previous mail as it was wrongly sent to an unrelated thread. --

Re: [gmx-users] COM Pull energy in v. 2016.1

False alarm, sorry. Indeed, the energies have the same sign. On 12/20/2016 10:56 AM, Alex wrote: I sent this question earlier, but I think it got lost somehow... I have two nearly identical simulations running on GMX 5.1.2 and GMX 2016.1. The COM pull energies in the logs have opposite

[gmx-users] COM Pull energy in v. 2016.1

I sent this question earlier, but I think it got lost somehow... I have two nearly identical simulations running on GMX 5.1.2 and GMX 2016.1. The COM pull energies in the logs have opposite signs, even though the pull code in the inputs is the same and basically the same process is taking

Re: [gmx-users] COM group of Membrane and Protein simulation

Dear Justin, Thank you very much. Sincerely, Mijiddorj > > -- > > Message: 5 > Date: Sun, 4 Dec 2016 18:04:16 -0500 > From: Justin Lemkul <jalem...@vt.edu> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] COM group of Membrane an

Re: [gmx-users] COM group of Membrane and Protein simulation

= com -- Message: 5 Date: Fri, 2 Dec 2016 07:50:52 -0500 From: Justin Lemkul <jalem...@vt.edu> To: gmx-us...@gromacs.org Subject: Re: [gmx-users] COM group of Membrane and Protein simulation Message-ID: <cc3fc878-feef-4424-dacd-

Re: [gmx-users] COM group of Membrane and Protein simulation

is better to the simulation? ; refcoord_scaling= com -- > > Message: 5 > Date: Fri, 2 Dec 2016 07:50:52 -0500 > From: Justin Lemkul <jalem...@vt.edu> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] COM group of Membran

Re: [gmx-users] COM group of Membrane and Protein simulation

and the peptide. Please suggest me with helpful options? How can I chose COM groups? -- > > Message: 5 > Date: Fri, 2 Dec 2016 07:50:52 -0500 > From: Justin Lemkul <jalem...@vt.edu> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] COM group

Re: [gmx-users] COM group of Membrane and Protein simulation

On 12/1/16 9:17 PM, Mijiddorj Batsaikhan wrote: Dear gmx_users, I started simulation that a peptide on membrane. My peptide locates on the membrane surface. I have two questions relating to the simulation. (1) When I start the simulation, I chose COM groups separately. Is this choice okay? or

[gmx-users] COM group of Membrane and Protein simulation

Dear gmx_users, I started simulation that a peptide on membrane. My peptide locates on the membrane surface. I have two questions relating to the simulation. (1) When I start the simulation, I chose COM groups separately. Is this choice okay? or May I need to chose COM group inseparately? (2)

Re: [gmx-users] COM-COM distance: PBC problem

Hi Arnost, When you fit with rotation the coordinates and the box are not on par anymore. Anything you do after that tries using PBC will fail. I guess that Plumed is trying to use the box to get the COM-COM distance. The only (practical) solution: don't fit. Cheers, Tsjerk On Aug 17, 2016

[gmx-users] COM-COM distance: PBC problem

Dear Plumed users, I've encountered one problem I'm unable to resolve. I use combination of Gromacs 5.0.4 and Plumed 2.1.3 and what I want is to calculate restrained distance between two center of masses (COMs) corresponding to two chains within a dimeric protein. If I let Plumed to calculate

[gmx-users] COM-Pull along a direction

Dear Gromacs users, I am trying to pull an ion out of a protein using Gromacs/5.0.4. I pull the ion along specific pre-determined paths. From my understanding, pulling along a direction _V guarantees that the dumb bead would move only at direction _V. The position of the dumb bead is

Re: [gmx-users] COM motion removal: diffusion analysis

On 12/28/15 10:28 AM, gromacs query wrote: Hi All I have protein-membrane system and gromacs tutorial by Justin suggests to do COM separately for protein_membrane and water. I am bit meesed up COM removal understanding. 1) I want to do diffusion analysis of protein in a membrane (2D/3D)

Re: [gmx-users] COM motion removal: diffusion analysis

>> It is not a matter of resetting positions; it is about subtracting falsely accumulated kinetic energy. Thanks, this is it :) On Mon, Dec 28, 2015 at 8:58 PM, Justin Lemkul wrote: > > > On 12/28/15 10:28 AM, gromacs query wrote: > >> Hi All >> >> >> I have protein-membrane

[gmx-users] COM motion removal: diffusion analysis

Hi All I have protein-membrane system and gromacs tutorial by Justin suggests to do COM separately for protein_membrane and water. I am bit meesed up COM removal understanding. 1) I want to do diffusion analysis of protein in a membrane (2D/3D) how it will influence my results if I perform it

Re: [gmx-users] COM motion removal

On 9/24/15 1:16 AM, Parvez Mh wrote: Hey gromacs users, When COM motion should be used in simulation? I followed in justin lemkul's gromacs tutorials of gromacs in internet. I found that he did not use COM motion removal in some of the simulation. Can any body tell me should i use and when

[gmx-users] COM motion removal

Hey gromacs users, When COM motion should be used in simulation? I followed in justin lemkul's gromacs tutorials of gromacs in internet. I found that he did not use COM motion removal in some of the simulation. Can any body tell me should i use and when should not? Regards Masrul -- Gromacs

Re: [gmx-users] Com pulling in reverse Z direction in SMD simulation..

On 4/24/14, 5:21 AM, Kalyanashis wrote: Dear all, I am doing SMD simulation of a enzyme system and I have given the pull option in Z direction. The com pulling options are given below, ;COM pulling pull = umbrella pull_geometry= distance pull_dim