[gmx-users] Fw: extremum value of rvdw rcoulomb rlist parameter

Hi what is them extremum value of three parameters, rvdw,rlist and rcoulomb in mdp file best of luck -- 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

[gmx-users] 2nd CfP EuroVis 2019 Workshop on Molecular Graphics and Visual Analysis of Molecular Data

* Workshop on Molecular Graphics and Visual Analysis of Molecular Data (co-located with EuroVis 2019), June 3, 2019, Porto, Portugal ** Molecular visualization is one of the oldest branches of scientific visualization,

[gmx-users] Clustsize and -mol option

Although I have successfully used clustsize for identifying clusters of atoms, I am stymied by the -mol option for evaluating clusters of molecules. A command such as: gmx clustsize -s system1.tpr -f system1.xtc -nc -n index.ndx Works fine for obtaining information about clusters of atoms,

Re: [gmx-users] COM

Hi, I already used index.ndx at the line of code but the error kept the same. I believe this is not the problem Thanks Laura Em ter, 22 de jan de 2019 às 16:25, Joaquim Rui de Castro Rodrigues < joaquim.rodrig...@ipleiria.pt> escreveu: > Hi, > > Your command line specifies -n fix.ndx but you

[gmx-users] Rotation matrix sequence

Dear all, I´m using g_rotmat to calculate the angles and therefore orientation of a protein after simulation. However, I cannot find any information on the documentation regarding which rotation sequence does GROMACS use for computing the rotation matrix. I´m assuming an RzRyRx sequence (first

Re: [gmx-users] COM

Hi, Your command line specifies -n fix.ndx but you seem to be editing a file named "index.ndx". HTH, Rui Rodrigues De: gromacs.org_gmx-users-boun...@maillist.sys.kth.se em nome de laura O. Enviado: 22 de janeiro de 2019 17:31 Para:

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

Re: [gmx-users] "Too many LINCS warnings" in a minimization after solvation with coarse-grained waters

Hello Cheng, The lines at the end of this mail are the extra parameters we usually define in our lab whenever we need to use soft potentials. They are based on the parameters given by CHARMM-GUI for the Martini Maker.  However, you *may* need to make alterations if there are conflicts with

[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] delay at start

hi, i notice that gromacs, when i start an MD simulation usuallyspends up to a few minutes using only one (out of several possible) threads.after a while it seems to have figured something out and then starts to runusing more threads. This is particularly conspicuous if also GPU is used.It is

Re: [gmx-users] turning off non-bonded terms

Thank you Justin. Kind regards, Ali -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se On Behalf Of Justin Lemkul Sent: dinsdag 22 januari 2019 15:59 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] turning off non-bonded terms On 1/22/19 9:37 AM, Ali

Re: [gmx-users] seeking help for generating combined trajectory files and clusters

Hi, I can't tell, because I don't know what you did with the xtc files beforehand. But you should follow my earlier advice and visualize the combined trajectory and observe that this may be your problem before talking about it further. :-) Then see

Re: [gmx-users] seeking help for generating combined trajectory files and clusters

Hi Mark, yes that makes sense. Then how can I make trjconv avoid from writing protein+ligand in different cells? Ming On Tue, Jan 22, 2019 at 9:59 AM Mark Abraham wrote: > Hi, > > No, length has nothing to do with whether mdrun or trjconv may have written > different rounds in different

Re: [gmx-users] turning off non-bonded terms

On 1/22/19 9:37 AM, Ali Khodayari wrote: Dear Users, Does it make sense if I use rcoulomb = 0 and rvdw = 0 in order to turn off non-bonded term calculation during mdrun? If not, is there any recommendations? That does the opposite - setting cutoffs to zero calculates *all* nonbonded

Re: [gmx-users] seeking help for generating combined trajectory files and clusters

Hi, No, length has nothing to do with whether mdrun or trjconv may have written different rounds in different representations (e.g. protein+ligand in the same periodic cell, or different cells). Mark On Tue, 22 Jan 2019 at 15:40 MD wrote: > Thanks Mark. > When you said "mutually compatible

Re: [gmx-users] "Too many LINCS warnings" in a minimization aftersolvation with coarse-grained waters

Depends on your itp file. If you look in martini_v2.2P.itp at the definition of WP (polarized water) for example, you can see its constraints are wrapped as such: #ifdef FLEXIBLE ; for minimization purposes constraints might be replaced by stiff bonds [ bonds ] 1 2 1 0.14 1 1 3 1 0.14 1

Re: [gmx-users] seeking help for generating combined trajectory files and clusters

Thanks Mark. When you said "mutually compatible periodic representation", did you mean they all have to have the same length of simulation? E.g. if one of them has a different length (91ns) and the rest all have 90 ns, the combining process will go wrong? On Tue, Jan 22, 2019 at 4:13 AM Mark

[gmx-users] turning off non-bonded terms

Dear Users, Does it make sense if I use rcoulomb = 0 and rvdw = 0 in order to turn off non-bonded term calculation during mdrun? If not, is there any recommendations? Thank you for your responses in advanced. Kind regards, Ali -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] "Too many LINCS warnings" in a minimization after solvation with coarse-grained waters

Dear Fotis and Peter, Thank you very much for the help. Fotis, Can I modify the mdp file to use "soft" potential modifier, how to do that? I think my problem is not the first reason (i.e. something wrong with the system structure or topology), because the potential is decreasing for the

Re: [gmx-users] Error Found by Equilibration

Thank you very much. Lianxin -- 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] "Too many LINCS warnings" in a minimization after solvation with coarse-grained waters

Hi all, @Fotis, the softcore potential for minimization sounds interesting, I'll remember that! Alternatively, something we also occasionally do in the lab, is replace all constraints for stiff bonds during minimization and if needed the first bit of equilibration. Peter On 22-01-19 13:24,

Re: [gmx-users] "Too many LINCS warnings" in a minimization after solvation with coarse-grained waters

Hello all, I would like to point out step 2 of the original poster's message: /2) Then 10 of this protein were inserted to a box, followed by a />>/minimization. It "stopped because the algorithm tried to make a new step />>/whose size was too small, or there was no change in the energy

[gmx-users] GROMACS 2018.5 patch release available

Hi GROMACS users, The official release of GROMACS 2018.5 is available! This release fixes several issues found since 2018.4. We encourage all users of the 2018 series to update to 2018.5. Please see the link to the release notes below for more details. You can find the code, documentation,

Re: [gmx-users] "Too many LINCS warnings" in a minimization after solvation with coarse-grained waters

Hi, You can reduce the timestep during equilibrations to e.g. 10 fs, or 5 when you have a really bad starting configuration. Bring it back up to 20 (in steps if needed) before starting your actual equilibration/production though. In addition, you can raise the lincs_order to 8. And yes, the

Re: [gmx-users] Error Found by Equilibration

Hi, Minimization is sometimes not enough to stop http://manual.gromacs.org/current/user-guide/terminology.html#blowing-up. Start with a smaller timestep while you let the large forces relax. Then move to your production setup. Mark On Tue, 22 Jan 2019 at 01:02 Lianxin Xin wrote: > Hi,

Re: [gmx-users] seeking help for generating combined trajectory files and clusters

Hi, You're comparing to the configurations in -f2, but that will only make sense if the contents of the files for each round have mutually compatible periodic representation. I suggest you visualise the combined trajectory and observe the problem. Mark On Mon, 21 Jan 2019 at 17:30 MD wrote: >

Re: [gmx-users] "Too many LINCS warnings" in a minimization after solvation with coarse-grained waters

Hi, I don't have any experience of coarse-grained systems, but everything looks OK from this level. It is normal to troubleshoot by visualizing your input and progress result. Minimizers are local, so if you start from something that has a frustration that can't be resolved, you are stuck.

Re: [gmx-users] npt equlibration without position restrain

Thank you very much for your help. Olga ‫בתאריך יום א׳, 20 בינו׳ 2019 ב-22:35 מאת ‪Mark Abraham‬‏ <‪ mark.j.abra...@gmail.com‬‏>:‬ > Hi, > > They're inactive so whether they have any value or are present does not > matter. > > Mark > > On Sun., 20 Jan. 2019, 10:34 Olga Press, wrote: > > > Dr.