[gmx-users] Re: Aspartate at high pH

Thank you Tsjerk! -- View this message in context: http://gromacs.5086.n6.nabble.com/Aspartate-at-high-pH-tp5005500p5005502.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gm

[gmx-users] Re: Error: Atoms in the .top are not numbered consecutively

Hi Henri, Have you been able to solve this problem? Best, Valentina -- View this message in context: http://gromacs.5086.n6.nabble.com/Error-Atoms-in-the-top-are-not-numbered-consecutively-tp4429383p5005573.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx

[gmx-users] Re: initial temperature ridiculously high

Hi Guozhen, I know it has been a while, BUT I am having same/similar problem with CLAYFF. I start with a configuration optimised by CASTEP. Have you found a solution? Did you continue using CLAYFF? I have a ClayFF.ff available, if you want to compare. Thanks,V -- View this message in context:

[gmx-users] Re: g_x2top help

Hi Millinda. I know it is an old post, bt I am not sure if your defaults are correct. This question is only because I am struggling to make CLAYff work and hence looking around. So mb you know something I don't. > [ defaults ] > ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ >

[gmx-users] generating user-defined topologies for surfaces

Hello, I have a strange question with regard to set up of a FF for pdb2gmx for inorganic surfaces (or dendrimers). So previously I used ClayFF (i.e. non-bonded FF) and written input for pdb2gmx - no problem there. Now I want to use the bonded FF. So I have a unitcell, a residue in what gromacs kn

[gmx-users] Re: generating user-defined topologies for surfaces

Great, thank you, Justin. -- View this message in context: http://gromacs.5086.x6.nabble.com/generating-user-defined-topologies-for-surfaces-tp5010192p5010195.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://li

[gmx-users] Re: generating user-defined topologies for surfaces

A follow up question - does searching for neighbouring atoms to bond to according to specbond.dat slow down calculation and if so how significantly. Thanks! -- View this message in context: http://gromacs.5086.x6.nabble.com/generating-user-defined-topologies-for-surfaces-tp5010192p5010196.ht

[gmx-users] Re: generating user-defined topologies for surfaces

Thank you. So it is only involved in pdb2gmx, but not in the simulation itself - perfect. For some reason I assumed it is checked through the simulation. Writing it now. -- View this message in context: http://gromacs.5086.x6.nabble.com/generating-user-defined-topologies-for-surfaces-tp5010192

[gmx-users] Re: generating user-defined topologies for surfaces

Sorry, still confused here: I have a cell, that is same as residue, contains an inorganic crystal. But since I am creating a surface I have bonds going across periodic boundary, like Al and O shown on the pic? Can I still do it? How do I input it into molecule.rtp? Thank you, V

[gmx-users] Re: generating user-defined topologies for surfaces

perfect! -- View this message in context: http://gromacs.5086.x6.nabble.com/generating-user-defined-topologies-for-surfaces-tp5010192p5010235.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/m

[gmx-users] general question about molecule.rtp and pdb2gmx

Hi, a general question about writing molecule.rtp and how pdb2gmx treats it. I have a few atom types and a few atoms per each atom type. So a question - when I define interactions, say [ bonds ] can I define them by atomtype, rather that atom number?! *So like this:* [ B31 ] [ atoms ] ; atomn

[gmx-users] Re: general question about molecule.rtp and pdb2gmx

Ok, thank you! I was hoping for an easier job. My system is anyhow flying apart - trying to spot a problem. Hence trying. One more question - [ pairs ] get automatically generated. But I don't need 1-4 LJ. So I can just remove them? Thank you -- View this message in context: http://gromacs.

[gmx-users] Re: general question about molecule.rtp and pdb2gmx

Yes - own parameters. Just thought gen-pairs in [ defaults ] should prevent this output. Thank you -- View this message in context: http://gromacs.5086.x6.nabble.com/general-question-about-molecule-rtp-and-pdb2gmx-tp5010759p5010764.html Sent from the GROMACS Users Forum mailing list archive at

[gmx-users] Re: Creating an infinite sheet of graphene

Hi, I have no answer to this question, sorry. But I am trying to simulate the layered structure (also with periodic_molecule = yes) I am getting error: Steepest Descents: Tolerance (Fmax) = 1.0e+01 Number of steps= 500 A list of missing interactions: exclusi

[gmx-users] periodic_molecule & missing interactions

I have a layered double hydroxide structure: i.e a sheet with Metals (Al & Mg), that are balanced by OH groups on both sides. The sheet should be periodic in xy-direction and there are bonds between Al and OH. For this, obv., I am using in-house FF, that I assign with pdb2gmx. In the molecule.

[gmx-users] Re: periodic_molecule & missing interactions

Thank you for your reply. My box is quite small indeed, so my cut-offs are 0.5 If I make a single layer, I would have to run quite a small system in z-direction. My residue box size:0.62840 0.54421 1.6 0.0 0.0 -0.31420 0.0 0.0 0.0 My suspect of the pro

[gmx-users] periodic molecule

Hello! I have a surface, formed by Mg2Al(OH)6. All of the O are bonded with Al, by such forming a mesh. I am using periodic_molecule=yes as discussed in this thread: http://gromacs.5086.x6.nabble.com/generating-user-defined-topologies-for-surfaces-td5010192.html#a5010234 I set up the topology fo

[gmx-users] Re: Why do you delete the messages?

You mean this one? http://gromacs.5086.x6.nabble.com/The-computational-methods-used-in-Gromacs-td5011269.html you have posted it in Gromacs general forum, but checking for it in Gromacs Users forum (i.e sub-forum) hence don't see it! V -- View this message in context: http://gromacs.5086.x6.

[gmx-users] Re: periodic molecule

Thank you! Yep, they seem to be wanting to bond to the O's within the cell, while they are meant to bond across the PBC. I am not sure how periodic_molecule = yes part functions. I don't seem to get difference if I turn it on or off when I do Energy minimisation. Do you have some examples that wo

[gmx-users] Re: periodic molecule

Justin Lemkul wrote > On 9/18/13 8:07 AM, Valentina wrote: >> Thank you! >> >> Yep, they seem to be wanting to bond to the O's within the cell, while >> they >> are meant to bond across the PBC. >> >> I am not sure how periodic_molecule = yes part

[gmx-users] Re: periodic molecule

Thank you, Yes. The bond between Al and O is 1.96 A So it should be within 10% from 2.06 A, so the lowest size is 1.854 A? It should be able to pick up 1.96 A then. Am I right? -- View this message in context: http://gromacs.5086.x6.nabble.com/periodic-molecule-tp5011270p5011284.html Sent from

[gmx-users] Re: periodic molecule

Bonds are harmonic. I can test it by restraining them? For purpose of testing I can even make the topology bond to be 2.06, as in the input file. My system shouldn't be any different from a mice sheet, for instance. Both have Metal - O bonds that continue through the sheet. What do you mean by "t

[gmx-users] Re: periodic molecule

On restraining bonds: The atom moves across the basic unit, i.e. it is not recognising that it should bond via periodic_molecule Error: The charge group starting at atom 2833 moved than the distance allowed by the domain decomposition (1.615483) in direction X In any case (restraining or not all

[gmx-users] Re: periodic molecule

Update https://docs.google.com/file/d/0B6Qm4snFANimcmxYVnBOSkNCd2s/edit?usp=sharing Seems I had to declare the atoms in .rtp with + and - when they are across periodic boundary. The new movie is showing that atoms do move, but not across the box. Yes, I would have to play a little ore with param

[gmx-users] Re: periodic molecule

OK seems it is my self-post, but incase anyone finds it, so they are not mislead by the above. After few more trial and fails, I think currently there is no tool to assemble a periodic system from "residues". So neither the approach with specbonds, nor the periodic_molecule work for this case. Hen

[gmx-users] Could not find force field in current directory

ldh21-edit.pdb ldh21.pdb residuetypes.dat Could you, please, indicate where the problem may be? Many thanks, Valentina __ Dr Valentina Erastova Postdoctoral Research Assistant Department of Earth Sciences Durham University Edito

Re: [gmx-users] Could not find force field in current directory

Thank you for your reply Justin, it is 4.5.5 ( i haven't yet got to instal 4.6 yet) i tried it on Mac and Linux. Shall I attach the files, may be? I have earlier written another forcefield and it worked without problems. Kind regards, Valentina __ Dr Vale

Re: [gmx-users] Could not find force field in current directory

Just a follow up. I have also tried using g_x2top and I am getting the same error. Kind regards, Valentina __ Dr Valentina Erastova Postdoctoral Research Assistant Department of Earth Sciences Durham University Editor-in-Chief, Kaleidoscope +44 786 131 6686 On 23

Re: [gmx-users] Could not find force field in current directory

Awesome. Thank you very much. I will email you a zip. Kind regards, Valentina __ Dr Valentina Erastova Postdoctoral Research Assistant Department of Earth Sciences Durham University Editor-in-Chief, Kaleidoscope +44 786 131 6686 On 23 Jan 2013, at 18:47, Justin

Re: [gmx-users] Could not find force field in current directory

Ooops, thank you very much! Dyslexic people & computers are not a good combination! Valentina On 23 Jan 2013, at 19:03, Justin Lemkul wrote: > > > On 1/23/13 1:50 PM, Valentina Erastova wrote: >> Awesome. Thank you very much. >> I will email you a zip.

Re: [gmx-users] Could not find force field in current directory

Hi Alexey, Justin found my error - ooops - misspelled one of the filenames. Thank you for your reply! Valentina On 23 Jan 2013, at 19:50, Alexey Shvetsov wrote: > Hi! > > What files do you have in .ff directory? > > Do you have files > ffbonded.itp ffnonbonded.i

[gmx-users] Aspartate at high pH

Hello! I am simulating Aspartate at pH > 10, so it needs to be fully deprotonated (COO-, COO- and NH2). pdb2gmx allows to easily set side chains to be deprotanted, but is there a straightforward way to make NH2, not NH3+? Thank you very much! Kind regards, Valent

[gmx-users] pdb2gmx

Hello all, I am converting a .pdb into .gro and .top and assigning ClayFF forcefield, that is not included in the gromacs. It's a strange FF as doesn't have ones between all of the atoms, just O-H but it has an angle between a metal and OH, therefore I wore out molecule.rtp (see below) that i

[gmx-users] installation on mac os x snow leopard

: Cannot find fftw3f library ~~~ Valentina Tozzini NEST-INFM-CNR, Scuola Normale Superiore Piazza San Silvestro, 12 - 56127 Pisa (PI) - Italy Phone: +39 050 509 433Fax: +39 050 509 417 Email: tozz...@nest.sns.it

Re: [gmx-users] installation on mac os x snow leopard

thank you, it worked. On Jan 7, 2010, at 12:20 PM, Erik Marklund wrote: > Valentina Tozzini skrev: >> dear all >> has anybody tried to install gromax (vs 4.0.7) on mac os x snow leopard >> (10.6.2)? >> I have the following problem: the configure script does not work.