Re: [gmx-users] six member ring won't stay flat

On Tue, Jan 16, 2018 at 6:43 AM, Mark Abraham wrote: > Hi, > > You still have many sources of problems (e.g. the warnings you suppressed, > the fact that your ring's atoms interact with an environment). What happens > when you minimize a capped peptide in vacuo? > ​Hi

Re: [gmx-users] rlist- group scheme

Hi Mark, For rlist=rcut-off (max one) it works correctly, but as soon as rlist> rcut-off it fails and gives different energies. Which I do not understand why. In principle, there is nothing going on after cut-off in potentials. Best regards On Sat, Jan 20, 2018 at 1:13 AM, Mark Abraham

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 165, Issue 93

Using the "grep" command in the force field forlder (/usr/local/gromacs/share/gromacs/top/charmm27.ff$ , for example "grep MG" or "grep Mg" can help. 2018-01-20 11:00 GMT+00:00 < gromacs.org_gmx-users-requ...@maillist.sys.kth.se>: > Send gromacs.org_gmx-users mailing list submissions to >

Re: [gmx-users] rlist- group scheme

Hi, Yes, you said that before. But I asked what range it worked over, ie what range of cutoff. Mark On Sat, Jan 20, 2018, 17:15 Faezeh Pousaneh wrote: > Hi Mark, > > For rlist=rcut-off (max one) it works correctly, but as soon as rlist> > rcut-off it fails and gives

Re: [gmx-users] How to solve this fatal error?

Hi order of element? 2018-01-20 15:59 GMT-08:00 Mark Abraham : > Hi, > > Like the message says, you have mishandled the order of the elements of > your topology. Look at the examples in the documentation. > > Mark > > On Sun, Jan 21, 2018, 00:40 حلیمه میرسالاری

[gmx-users] How to solve this fatal error?

Dear all l am using gromacs 4.5.5 version for simulation carbon nanotubes in tip3p water with charmm27 force feild. I used grompp for energy minmization,but l encountered with fatal error: [ file tip3p.itp, line 40]: Atom index (1) in settles out of bounds (1-0). This probably means that you

Re: [gmx-users] How to solve this fatal error?

Hi, Like the message says, you have mishandled the order of the elements of your topology. Look at the examples in the documentation. Mark On Sun, Jan 21, 2018, 00:40 حلیمه میرسالاری wrote: > Dear all > > l am using gromacs 4.5.5 version for simulation carbon

[gmx-users] (no subject)

Dear all, I am a beginer. I would like to know the purpose of adding ions during the simulation process. -- 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

Re: [gmx-users] six member ring won't stay flat

Hi, Sorry, I can't remember what you've said your workflows may once have been... Mark On Sat, Jan 20, 2018, 13:46 MD wrote: > On Tue, Jan 16, 2018 at 6:43 AM, Mark Abraham > wrote: > > > Hi, > > > > You still have many sources of problems (e.g.

Re: [gmx-users] How to solve this fatal error?

Hi, Element, as in small thing from which bigger things are made. See http://www.gromacs.org/Documentation/Errors#Atom_index_(1)_in_bonds_out_of_bounds Mark On Sun, Jan 21, 2018, 01:26 حلیمه میرسالاری wrote: > Hi > order of element? > > > 2018-01-20 15:59 GMT-08:00

Re: [gmx-users] (no subject)

You need some ions to neutralise the system for long range electrostatics to work. We usually add more to make the simulation more like the real system (solution or cell). > On Jan 21, 2018, at 1:12 AM, Sankaran SV . <119013...@sastra.ac.in> wrote: > > Dear all, > >I am a beginer.

Re: [gmx-users] (no subject)

A beginner in what? Your question has nothing to do with Gromacs. Alex On 1/20/2018 11:12 PM, Sankaran SV . wrote: Dear all, I am a beginer. I would like to know the purpose of adding ions during the simulation process. -- Gromacs Users mailing list * Please search the