Re: [gmx-users] Gromacs 4.6 4.5.3 qualitative differences 4.6 instability in polarizable force field vacuum/liquid mixture interface simulations

Meulenhoff, Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, Michael Shirts, Alfons Sijbers, Peter Tieleman, Berk Hess, David van der Spoel, and Erik Lindahl. Copyright (c) 1991-2000, University of Groningen, The Netherlands

Re: [gmx-users] how to calculate kinetic constant?

/ct400404q -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman

Re: [gmx-users] Re: g_hydorder

a guess that I actually need sgmol/sgmean (variables as defined in program) as the final output. Please help me understand the usage of this command in order to fulfill my aim.I have posted this twice but have not got a single reply. Thanks in advance. -- David van der Spoel, Ph.D., Professor

Re: [gmx-users] confusion about implicint solvent

to recommend my latest paper which shows how solvent entropy and enthalpy contribute in a complex manner to non-bonded interactions in a way that implicit solvent never could: http://pubs.acs.org/doi/abs/10.1021/ct400404q -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol

Re: [gmx-users] Long range Lennard Jones

. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing list

Re: [gmx-users] perl scripts to convert CHARMM ff in GROMACS

? Could anyone help me with their scripts in this regard? http://www.gromacs.org/Downloads/User_contributions/Other_software Thank you for your help in advance. Regards, Revathi -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596

Re: [gmx-users] hessian calculation with periodic boundary condition

? Thanks! Best JT Yes it does. The parallel version is broken, by the way, a fix is underway. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se

Re: [gmx-users] Lipid Bilayer on the Graphene or GO substrate

the equilibrium distance between the periodic graphene and the periodic lipid bilayer in MD simulations. Best, Jason --- original message- Message: 2 Date: Thu, 08 Aug 2013 13:41:59 +0200 From: David van der Spoel sp...@xray.bmc.uu.se mailto:sp

Re: [gmx-users] Lipid Bilayer on the Graphene or GO substrate

, Jason -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman

Re: [gmx-users] BOND ... ANGLE and TORSION energy discrepancy between gromacs and cp2k

file have limited precision. the force constants you can check yourself. Thanks Golshan -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se

Re: [gmx-users] Lipid Bilayer on the Graphene or GO substrate

Date: Thu, 08 Aug 2013 08:37:15 +0200 From: David van der Spoel sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se Subject: Re: [gmx-users] Lipid Bilayer on the Graphene or GO substrate To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org Message-ID

Re: [gmx-users] Regarding gromos method in g_cluster

of structures for matrix 12501 Energy of the matrix is 960.075 nm Found 1 clusters Writing middle structure for each cluster to clusters.pdb Counted 0 transitions in total, max 0 between two specific clusters ## -- David van der Spoel, Ph.D., Professor

Re: [gmx-users] Regarding gromos method in g_cluster

see, then maybe the definition is different (check the source code!). It could be that it is 0.3 nm from the cluster center. On Wed, Jul 31, 2013 at 12:59 PM, David van der Spoel sp...@xray.bmc.uu.sewrote: On 2013-07-31 07:20, bipin singh wrote: Hello All, I was trying to do clustering on my

Re: [gmx-users] Limitations of simulations?

in J. Amer. Chem. Soc. a year or two ago. I have no formal experience with simulations and currently have no one around me with enough knowledge on these topic to mentor me, so any help is very much appreciated! Thank you! :) -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell

Re: [gmx-users] g_hbond for trajectory without having box information

: Fatal error: Your computational box has shrunk too much. g_hbond_mpi can not handle this situation, sorry. Please let me know, if there is any way to rectify this error. you can add a box to your trajectory using trjconv. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell

Re: [gmx-users] Re: g_velacc

the tradition ripples. If this is for water the result could be ok with 100 ps, but you still need to have decent sampling (e.g. 20 fs) of the velocities since they change rapidly. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala

Re: [gmx-users] FW: Inconsistent results between 3.3.3 and 4.6 with various set-up options

posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University

Re: [gmx-users] Re: g_velacc

in context: http://gromacs.5086.x6.nabble.com/g-velacc-tp5009541p5009543.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone

Re: [gmx-users] g_velacc

actually tried? You need to store the Velcoties quite often, maybe every 20 fs (depending on the system). Nepal -- View this message in context: http://gromacs.5086.x6.nabble.com/g-velacc-tp5009541.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- David van

Re: [gmx-users] How to modify the code g_hbond to analyze the non-traditional hydrogen bonds like C-H...O

would like to try to discourage modifications. That said, a small hack in search_donors() should do the trick. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp

Re: [gmx-users] ***using output of dl_poly in gromacs??***

is easy to make for proteins/nucleic acids. Run a gromacs tutorial if you haven't yet. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx

Re: Fw: [gmx-users] ***using output of dl_poly in gromacs??***

will be appreciated for some analysis you do not need it at all. For some analysis you could also leave out the metal (e.g. secondary structure of protein). - Forwarded Message - *From:* David van der Spoel sp...@xray.bmc.uu.se *To:* gmx-users@gromacs.org *Sent:* Wednesday, 26 June 2013, 11:10 *Subject

Re: [gmx-users] Re: Enthalpy Confusion

.x6.nabble.com/Enthalpy-Confusion-tp5009053p5009164.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp

Re: [gmx-users] Re: Enthalpy Confusion

-tp5009053p5009168.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx

Re: [gmx-users] Re: Enthalpy Confusion

the GROMACS Users Forum mailing list archive at Nabble.com. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users

Re: [gmx-users] Enthalpy Confusion

archive at Nabble.com. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http

Re: [gmx-users] Re: Enthalpy Confusion

: http://gromacs.5086.x6.nabble.com/Enthalpy-Confusion-tp5009053p5009062.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205

Re: [gmx-users] why mass and charge is zero?

-7.758 I am a little bit confused for this. Does anybody have any idea for it? the ones in the atoms section are the ones that are used UNLESS they are not given, in which case the defaults are used. thank you very much best Albert -- David van der Spoel, Ph.D., Professor of Biology Dept

Re: [gmx-users] xx of the xxxx bonded interactions couldn't be calculated

-- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx

Re: [gmx-users] ngmx not installed in gmx4.6.1

Choudhury NCL, Pune INDIA -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http

Re: [gmx-users] viscosity

/SSAU1reN/ener.html. That website does not work. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users

Re: [gmx-users] Viscosity

your system and how you did the analysis. Did you use the same energy file with the different gromacs versions? In that case they should give the same result. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone

Re: [gmx-users] viscosity

me, please. I used the same energy file (ener.edr) and I get this results: http://help-gromacs.blogspot.com.br/. The files visco.xvg are equals. Maybe you can post the energy file on that site as well. Have you tried to compute the pressure autocorrelation (using g_energy)? -- David van der

Re: [gmx-users] Dihedral Autocorrelation Function with negative values

: Molecular dynamics simulations of Leu-Enkephalin in water and DMSO Biophys. J. 72 pp. 2032-2041 (1997) -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp

Re: [gmx-users] choice of forcefield

)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden

[gmx-users] Re: choice of force field -reg

. There are quite some resources out there. You might also look for Jochen Hub's web site. Thank you so much once again. Yours sincerely, Revathi M.S.Research Scholar Indian Institute of Technology Madras India -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol

Re: [gmx-users] Comparing Charmm 27 energies from GROMACS and NAMD

/Support/Mailing_Lists -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http

Re: [gmx-users] Fw: probability from COM of micelle

as following: density = g(r) * (N/V) It sounds like all you need to do is create a histogram from data produced by g_dist. You can make the histogram with g_analyze or any number of other programs. -Justin How about g_rdf? -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec

Re: [gmx-users] Including polarizability by a Drude oscillator or the shell model

DeYoung Carnegie Mellon University Check here for some examples http://virtualchemistry.org/pol.php -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp

Re: [gmx-users] Water spreading on graphene!

MDP File End # -- View this message in context: http://gromacs.5086.x6.nabble.com/Water-spreading-on-graphene-tp5007497.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala

Re: [gmx-users] Re: Water spreading on graphene!

simulations and to have this problem stumps me!! Thanks for being helpful always. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users

Re: [gmx-users] Re: Water spreading on graphene!

. You did not explain the charges on graphene. Sapna On Sun, Apr 21, 2013 at 12:14 PM, David van der Spoel sp...@xray.bmc.uu.sewrote: On 2013-04-21 12:39, Dr. Vitaly Chaban wrote: Yes, the water droplet should remain a droplet on graphene. Since you have a droplet, I assume you have much

Re: [gmx-users] pdb2gmx for small molecules?

Try GAFF using the Ambertools and acpype. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] Re: thermal conductivity,specific heat,enthalpy

Firstly I calculated Entalphy (16) Afterward I calculated both Etot (7) and pV (15) Enthalpy=Etot+pV Unfortunately, I get Enthalpy isnt equals to Etot+pV. Why? -- Ahmet Yıldırım -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124

Re: [gmx-users] Dihedral angle PCA

information on the structures. But this is for you to decide :). -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing list

Re: [gmx-users] Normal Mode Analysis -- Expected Output

Murtola, Szilard Pall, Sander Pronk, Roland Schulz, Michael Shirts, Alfons Sijbers, Peter Tieleman, Berk Hess, David van der Spoel, and Erik Lindahl. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2012,2013

Re: [gmx-users] Memory requirement to store trajectories

of gromacs? Also please suggest me if there is any other better approach to determine an estimate of hard disk space required. Thanks Sikandar grompp prints it for you if it is more than a certain amount (2 Gb I think). -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol

Re: [gmx-users] GROMACS 4.6 with GPU acceleration (double presion)

acceleration in the coming version of GROMACS or this will not happen in the nearest future. The hardware does not support it yet AFAIK. Thanks and regards, Mikhail -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden

Re: [gmx-users] Lipids and virtual site in 4.6.1

at Nabble.com. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org

Re: [gmx-users] Lipids and virtual site in 4.6.1

On 2013-04-08 11:52, David van der Spoel wrote: On 2013-04-08 11:34, Bastien Loubet wrote: Dear GROMACS user, Last week I was watching the GTC talk from Eric Lindahl, and I noticed his insistence on virtual site to accelerate simulation (up to 5ps time step). As a matter of fact our group

Re: [gmx-users] Free energy landscape by g_sham

-- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx

Re: [gmx-users] Re: diffusion constant level off

in advance -- Ahmet Yıldırım -- Ahmet Yıldırım -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users

Re: [gmx-users] How to specify water molecules number added to box?

) added into my system. Does it has anything with -ci and -nmol options of the program genbox? Your reply would be appreciated. genbox -h try -maxsol Thanks, Zhikun, from USTC -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124

Re: [gmx-users] Treating electrostatics and van der Waals interactions differently

! -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx

Re: [gmx-users] Dihedral restraints in 4.6 vs 4.5.X

requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone

[gmx-users] Fwd: [gmx-developers] Simulated annealing problem

This is a user problem, not a development problem. Original Message Subject: [gmx-developers] Simulated annealing problem Date: Thu, 14 Mar 2013 10:15:39 +0530 From: Gaurav Jerath g.jer...@iitg.ernet.in Reply-To: Discussion list for GROMACS development

[gmx-users] Postdoc jobs developing gromacs etc.

If you are interested in a gromacs-related development position at the postdoc level, please have a look at our ad below. Please spread to interested colleagues. http://www.uu.se/jobb/others/annonsvisning?languageId=1tarContentId=235221 Regards, -- David van der Spoel, Ph.D., Professor

Re: [gmx-users] Small bug with -pi in g_mindist?

that is unlikely to affect many users, but given the prevalence of non-rectangular boxes and the observation of previous complaints about mindist in the user list, I thought it would be good to report. Please let me know if I made an error anywhere! Best, Reid -- David van der Spoel, Ph.D

Re: [gmx-users] Whether CHARMM force field in GROMACS is different from that in CHARMM commercial package

in advance Fayaz -- View this message in context: http://gromacs.5086.n6.nabble.com/Whether-CHARMM-force-field-in-GROMACS-is-different-from-that-in-CHARMM-commercial-package-tp5005524.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- David van der Spoel, Ph.D

Re: [gmx-users] Water models and diffusion coefficient

reproduce literature values for the model and some experimental data, dens, DHvap, then this is as good as it gets. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.se

Re: [gmx-users] Re: Water models and diffusion coefficient

, that is -trestart 31. Thanks, -- View this message in context: http://gromacs.5086.n6.nabble.com/Water-models-and-diffusion-coefficient-tp5005377p5005385.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- David van der Spoel, Ph.D., Professor of Biology Dept

Re: [gmx-users] get the center of a cluster using gromacs

or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp

Re: [gmx-users] Error in BlueGene

interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp

Re: [gmx-users] g_x2top is missing bonds

to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists try acpype iso g_x2top (this comes straight from the developer). -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala

Re: [gmx-users] gromacs 4.6 GB/SA problem and poor performance

. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo

Re: [gmx-users] how to convert a dodecahedric trajectory into a triclinic one?

. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo

Re: [gmx-users] how to indicate solvent flexibility?

is to use g_select, but then the analysis has to be done on each individual frame, not the trajectory. Dynamic selections will be more conveniently implemented in a future Gromacs version. -Justin -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala

Re: [gmx-users] Toy input system - MD simulation

but, could you help me? What would you recommend me? Do you have a toy input system? Thank you very much, Maria http://virtualchemistry.org -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp

Re: [gmx-users] how to convert CGenFF into .itp file?

and it already has complete necessary information for paramters and topology). Probably one can consider improve this script and export the output file as a single .itp file. Hey, it's open source. Let us know how it goes :). best Albert -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell

Re: [gmx-users] how to convert CGenFF into .itp file?

On 2012-12-26 20:29, Albert wrote: On 12/26/2012 07:53 PM, David van der Spoel wrote: Hey, it's open source. Let us know how it goes Sorry what I meant was: If you make a better version of the charmm2gromacs script, then please upload it to the website. Cheers, David. you can simple

Re: [gmx-users] Box Pressure on individual box walls

interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp

Re: [gmx-users] how to run charmm2gromacs-pvm.py correctly?

/cmap.itp(if genCMAP = True) It seems that the input file is a folder instead of a single file? I generate my ligand topology from the CGenFF website and I only get a .rst file THX -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box

Re: [gmx-users] where is the script?

best Albert It's posted on the website. http://www.gromacs.org/Downloads/User_contributions/Other_software You want this one: charmm2gromacs-pvm.py -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone

Re: [gmx-users] How to avoid adding ions close to ligand

is there any other way to achieve this? Trying different numbers for -seed option seems inefficient and is dependent on luck. Thanks, Yun Maybe your assumption is wrong? Run a long MD simulation and you will find out. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec

Re: [gmx-users] Different average H bonds with different g_hbond releases

-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se

Re: [gmx-users] strange protonate state

this problem? thank you very much. best Albert This makes sense! The environment is made for a neutral group, which you get by either having a K+ or a proton near the Asp. Normal pdb2gmx will give you the correct topology. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol

Re: [gmx-users] strange protonate state

On 2012-11-19 10:42, Albert wrote: On 11/19/2012 10:27 AM, David van der Spoel wrote: On 2012-11-19 09:57, Albert wrote: hello: I've got a K+ near an Asp residue. I found that If I include the K+ in H++ calculation, the Asp is deprotonated while it is protonated if I didn't include it. I

Re: [gmx-users] Fatal error: In the chosen force field there is no residue type for 'GLN' as a starting terminus

you have to make a topology for your protein WITHOUT ligand and then merge it in a text editor, or better use an #include ligand.itp -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp

Re: [gmx-users] Fatal error: In the chosen force field there is no residue type for 'GLN' as a starting terminus

rename and remove atoms. GAFF is an alternative but it will not give you exactly the same charges and LJ parameters. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.se

Re: [gmx-users] Fatal error: In the chosen force field there is no residue type for 'GLN' as a starting terminus

file for CGLN. You may have to smooth the charges to keep it neutral. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing

Re: [gmx-users] g(r) does not go to 1 at long r -- bug in g_rdf?

also file a bug if deemed necessary. Take care, Pablo Thanks for reporting. Can you please make a redmine issue of this and assign it to me? -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205

Re: [gmx-users] Strange form of RDF curve

, first side chain then water. -- View this message in context: http://gromacs.5086.n6.nabble.com/Strange-form-of-RDF-curve-tp5003001.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol

Re: [gmx-users] Re:problem with simulation of freezing of water

not necessarily work under extremes or produce useful results under those conditions. -Justin Try TIP4P/Ice -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp

Re: [gmx-users] Polarisation model

completely. It would be interesting to have such a comparison although I expect few significant differences. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp

Re: [gmx-users] Polarisation model

On 2012-11-07 11:24, Volker Lesch wrote: On 11/07/2012 11:19 AM, David van der Spoel wrote: On 2012-11-07 10:21, Volker Lesch wrote: Dear all, I am a new Gromacs user. In the past I used AMBER, but because of performance and technical reason I want to switch to Gromacs. Actually, I have one

Re: [gmx-users] a question on g_hbond

. Cheers, Acoot -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org

Re: [gmx-users] Cholesterol parameters (Charrm36) in GMX

charmm2gromacs-pvm.py on the gromacs website that you can download. Use with care. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx

Re: [gmx-users] Cholesterol parameters (Charrm36) in GMX

that comes out. Do it in an empty directory. Thank you for replying! yorquant 2012/11/1 David van der Spoel sp...@xray.bmc.uu.se On 2012-10-31 16:31, Yorquant Wang wrote: Hi GMX-users, Klauda et al (J. Phys. Chem. B, 2012, 116 (1), pp 203–210) recently provided Cholesterol parameters

Re: [gmx-users] Conceptual question about the representation of dihedral angles in Gromacs

, so you get 9 different ones, all in phase as well. On top of that is the Coulomb and Van der Waals interaction between the H, which will increase the barrier height (because the atoms are closest there). In other words the barrier is way too high. Thank you! Andrew -- David van der

Re: [gmx-users] Dipole moment

vectors at each 3 fs? The dipole moment of charged box is not defined, since if one ion hops over periodic boundary conditions to the next box the dipole makes an enormous jump. Thanks Nilesh -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala

Re: [gmx-users] The problem of converting CGenff parameters to those of Gromacs

://www.gromacs.org/Support/Mailing_Lists -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] Re: Pull code with pull_geometry = cylinder generates error: Distance of pull group 1 (4.030185 nm) is larger than 0.49 times the box size (3.012310)

interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.se

Re: [gmx-users] average velocity

of Physics, Chemistry and Pharmacy University of Southern Denmark Campusvej 55, 5230 Odense M, Denmark -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp

Re: [gmx-users] Polarisablity of water using Gromacs

modern models available from http://virtualchemistry.org. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users

Re: [gmx-users] About Lincs Algorithim for Cyclic Peptide

generation gen_seed= -1; random seed ; COM motion removal ; These options remove COM motion of the system nstcomm = 10 comm-mode = Linear comm-grps = System Thanks In Advance -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol

Re: [gmx-users] Pull code with pull_geometry = cylinder generates error: Distance of pull group 1 (4.030185 nm) is larger than 0.49 times the box size (3.012310)

-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se

Re: [gmx-users] Fatal error: Atomtype F not found

biomolecules or something like that. More organic molecules topologies can be found at http://virtualchemistry.org -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp

Re: [gmx-users] Experiences with Gromacs scaling on US supercomputer centers?

. Best, Michael Shirts Assistant Professor Department of Chemical Engineering University of Virginia michael.shi...@virginia.edu (434)-243-1821 -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone

Re: [gmx-users] Automatic calculations of forces in tabulated potentials?

that can do it easily. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org

Re: [gmx-users] Problem with OMP_NUM_THREADS=12 mpirun -np 16 mdrun_mpi

nodes runs 12 threads internally or not. Check your mpirun syntax. It may only give 16 cores to mdrun. If anyone knows about this, please let me know. Thanks for help. Best Regards, Jesmin -- Jesmin Jahan Tithi PhD Student, CS Stony Brook University, NY-11790. -- David van der Spoel, Ph.D

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