Re: [gmx-users] g_rdf problem

Hi André, Many thanks for you big help! 2015-07-31 22:32 GMT+08:00 André Farias de Moura : > Hi Zhenyu, > > yes, I see this behavior every time a site is buried within a large > structure, say a micelle or a lipid bilayer. > > RDF profiles yield the PMF profiles between the two species, so a valu

Re: [gmx-users] Fwd: DFTB implementation

Hi Justin, I read the manual and it mentions how to specify QM/MM parameters, but no detail is provided. Also it says 'GROMACS provides interfaces to several popular Quantum Chemistry packages', but I'm not very clear about what does 'interfaces' mean. According to my understanding, if we want to c

Re: [gmx-users] Error:EM did not converge while using polarizable ion

Using sol2 option in the force field, and double precision version of gromacs might help. Yi On Jul 31, 2015 7:15 PM, "折晓会" wrote: > Dear all, > > I am now trying to simulation polarizable LiCl solutions with Gromacs > 5.0.5, where SWM4-NDP water model and corresponding polarizable ion model > a

Re: [gmx-users] Building a Larger Liquid Phase - Truncate 'Vacuum'

On Fri, Jul 31, 2015 at 8:56 PM, Justin Lemkul wrote: > > > Particle decomposition was removed from the code a long time ago. There are > lots of places where work is split among threads. > Interesting. Now I've got some catching up to do with the documentation and code. Thanks, Justin! >> opt

Re: [gmx-users] Error:EM did not converge while using polarizable ion

On 7/31/15 7:15 PM, 折晓会 wrote: Dear all, I am now trying to simulation polarizable LiCl solutions with Gromacs 5.0.5, where SWM4-NDP water model and corresponding polarizable ion model are used. The force field files come from professor Spoel and can be found in the website http://virtualch

Re: [gmx-users] Fwd: DFTB implementation

On 7/31/15 5:12 AM, Zhenyu Meng wrote: Dear all, I plan to do some QM/MM simulation using GROMACS. I read some papers which mentioned using GROMACS to do SCC-DFTB but no detail is provided. I wonder whether GROMACS can fulfill DFTB calculation directly? Or do I need to install some other softwa

Re: [gmx-users] Building a Larger Liquid Phase - Truncate 'Vacuum'

On 7/30/15 3:14 PM, Elton Carvalho wrote: On Thu, Jul 30, 2015 at 1:34 PM, Justin Lemkul wrote: There are as many DD cells as there are (thread-)MPI processes. These can be further subdivided into multiple OpenMP threads. What I was talking about above is the use of only OpenMP, e.g. mdru

[gmx-users] Error:EM did not converge while using polarizable ion

Dear all, I am now trying to simulation polarizable LiCl solutions with Gromacs 5.0.5, where SWM4-NDP water model and corresponding polarizable ion model are used. The force field files come from professor Spoel and can be found in the website http://virtualchemistry.org/pol.php. During the si

Re: [gmx-users] Jump of drug to other side of lipid bilayer

Hi, I answered this question yesterday. Please check for replies and do not blindly re-post. Mark On Fri, 31 Jul 2015 08:51 Marzieh Saeedi Masineh wrote: > Dear,I have done a simulation of DMPC lipid bilayer for 50 ns which has 10 > drug molecules which were positioned in the water phase in th

Re: [gmx-users] Eccentricity of Reverse Micelle

maybe g_gyrate -moi On Fri, Jul 31, 2015 at 12:11 PM, Tyler Cropley wrote: > Dear Gromacs Users, > > Is there a way to calculate eccentricity of a reverse micelle directly in > GROMACs or is there a way to calculate the ratio of the major and minor > axis. > > Thank you, > Tyler Cropley > -- > G

[gmx-users] Eccentricity of Reverse Micelle

Dear Gromacs Users, Is there a way to calculate eccentricity of a reverse micelle directly in GROMACs or is there a way to calculate the ratio of the major and minor axis. Thank you, Tyler Cropley -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Maili

Re: [gmx-users] g_rdf problem

Hi Zhenyu, yes, I see this behavior every time a site is buried within a large structure, say a micelle or a lipid bilayer. RDF profiles yield the PMF profiles between the two species, so a value below unity stands for a repulsive region (in the thermodynamic sense, not in the mechanical sense) a

Re: [gmx-users] submitting gmx cluster

Dear Carsten, Micholas and Peter, Thank You very much your suggestions, now it works! Best wishes, Aniko 2015-07-31 14:58 GMT+02:00 Peter Stern : > Or you can simply create a file, say "input" with an option on each line > and then, > gmx something < input > > -Original Message- > From:

Re: [gmx-users] submitting gmx cluster

Or you can simply create a file, say "input" with an option on each line and then, gmx something < input -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Lábas Anikó Sent: Friday, July 31,

Re: [gmx-users] submitting gmx cluster

Hi Aniko, Another option is to use a HERE doc such as: gmx something << HERE 0 1 HERE which would execute the gmx command and give it as input: 0, a return character, and then 1 (with a return character also). Check the advanced bash-scripting guide for more details: http://tldp.org/LDP/abs/

[gmx-users] KTH Comput Biophysics

Hello, Anyone from SciLife lab here? Just curious who took the assistant professorship in computational biophysics at KTH posted in 2014, http://www.scilifelab.se/fellows/ Many thanks, Yao -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing

Re: [gmx-users] submitting gmx cluster

Hi Aniko, > On 31 Jul 2015, at 10:52, Lábas Anikó wrote: > > Dear Gromacs Users, > > I would like to submit my 'gmx cluster' job, but I don't know how can I > define in my command line the following two options, which normally appear > on the screen when I run gmx cluster on my head machine: >

[gmx-users] Fwd: DFTB implementation

Dear all, I plan to do some QM/MM simulation using GROMACS. I read some papers which mentioned using GROMACS to do SCC-DFTB but no detail is provided. I wonder whether GROMACS can fulfill DFTB calculation directly? Or do I need to install some other software? -- Sincerely, Mr. Meng Zhenyu Divisio

[gmx-users] DFTB implementation

Dear all, I plan to do some QM/MM simulation using GROMACS. I read some papers which mentioned using GROMACS to do SCC-DFTB but no detail is provided. I wonder whether GROMACS can fulfill DFTB calculation directly? Or do I need to install some other software? -- Sincerely, Mr. Meng Zhenyu Divisio

[gmx-users] submitting gmx cluster

Dear Gromacs Users, I would like to submit my 'gmx cluster' job, but I don't know how can I define in my command line the following two options, which normally appear on the screen when I run gmx cluster on my head machine: 1. "Select group for least squares fit and RMSD calculation" 2. "Select gr