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

r Kasson, Carsten Kutzner, Per Larsson, Pieter 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, Un

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

.1021/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.or

Re: [gmx-users] Re: g_hydorder

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 of Biology Dept. of Cell

Re: [gmx-users] confusion about implicint solvent

portant. I would like 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 De

Re: [gmx-users] Long range Lennard Jones

cs.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.

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

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.u

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

w in the timescale of > MD simulations. The system seems to be time-consuming to find the > equilibrium distance between the periodic graphene and the periodic > lipid bilayer in MD simulations. > > Best, > Jason > > --- original message--------- >

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

t; Best, > Jason > > --- original message > --- > > Message: 1 > Date: Thu, 08 Aug 2013 08:37:15 +0200 > From: David van der Spoel <mailto:sp...@xray.bmc.uu.se>> > Subject: Re: [gmx-users] Lipid Bilayer on the Graphene or GO substrate > To: Discussion lis

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.u

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

on. Best, 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.groma

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

cluster. I 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 wrote: On 2013-07-31 07:20, bipin singh wrote: Hello All, I was trying to do clustering on my MD

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

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] Limitations of simulations?

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] FW: Inconsistent results between 3.3.3 and 4.6 with various set-up options

ttp://www.gromacs.org/Support/Mailing_Lists/Search before 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.

Re: [gmx-users] Re: g_velacc

ow 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

Re: [gmx-users] Re: g_velacc

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. P

Re: [gmx-users] g_velacc

iling 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@gromacs.org http://lists.gr

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.se

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

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 *To:* gmx-users@gromacs.org *Sent:* Wednesday, 26 June 2013, 11:10 *Subject:* Re: [gmx-users

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

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.

Re: [gmx-users] Re: Enthalpy Confusion

nabble.com/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.

Re: [gmx-users] Re: Enthalpy Confusion

essage in context: http://gromacs.5086.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, 7

Re: [gmx-users] Re: Enthalpy Confusion

5009053p5009068.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.bm

Re: [gmx-users] Re: Enthalpy Confusion

ibrium of course. -- View this message in context: 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.

Re: [gmx-users] Enthalpy Confusion

um 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-use

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. of

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

ons] -rdd 1.25 -Justin -- 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.gro

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

Re: [gmx-users] viscosity

/file/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 list

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] 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. P

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.se

[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 & Mo

Re: [gmx-users] choice of forcefield

e 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.

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

== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use t

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

), I do 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 Ce

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

o much for your time! Andrew 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..

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 wrote: 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 vacuum in the system. I

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

ve done so many 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://foldi

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

O GRO 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.

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

orce_Field -Justin 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 list

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

(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 Uppsala,

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

rr file 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 &am

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] 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

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, Sw

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] Lipids and virtual site in 4.6.1

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

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

archive at http://www.gromacs.org/Support/Mailing_Lists/Search before 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 Spo

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

e -- 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@gr

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.

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

t (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. Box 596, 7512

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-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 Reply-To: Discussion list for GROMACS development To: gmx-develop...@gromacs.org Hi, I am try

[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=1&tarContentId=235221 Regards, -- David van der Spoel, Ph.D., Professo

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] Is gromacs4.6 incompatible with some old tpr files?

ne find out what happened? Input file can be > downloaded at http://www.hpcchina.org/doc/gromacs_workload.tar.gz > > > Thanks~ > I have created a bug report http://redmine.gromacs.org/issues/1156 since I could reproduce the bug. Thanks for reporting. -- David van der Spoel, Ph.D.

Re: [gmx-users] ions.itp file for polarized ions

directive exclusions Please help me to deal with this issue? remove the exclusions. Since there are no bonds you can not have exclusions. Exclusions will nevertheless be generated. Please check the topology using gmxdump. Thanks a lot in advance. Best regards, Cuong -- David van der S

Re: [gmx-users] Parametrization of Arsenic

edit the topology to replace the P by As again, and modify the parameters such that the bond lengths and angles match the ones you get from QM. Are you sure this is a stable molecule by the way? I would expect it to loose at least one proton in solution. -- David van der Spoel, Ph.D

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

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] 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] 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.u

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

...@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] g_x2top is missing bonds

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 try acpype iso g_x2top (this comes straight from the developer). -- David van der Spoel, Ph.D., Professor of Biolo

Re: [gmx-users] Error in BlueGene

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: +46184714205.

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/list

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

to do anything. -- 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.o

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

groups 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., Uppsa

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

, 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

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 s

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

rom the offline FF 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., Prof

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

se 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: +46184714205. s

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

9optfoldername/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

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 & M

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

much 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,

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

.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] 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 inc

Re: [gmx-users] strange protonate state

solve 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 &am

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

orrect topology file. Now 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 Upp

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

; with help from the rtp 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://foldin

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

e top file 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...@

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

I think you need to switch the arguments, 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

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

I can 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: +46

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

hey do 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

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] 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.se

Re: [gmx-users] a question on g_hbond

your reply. 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://lis

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

r it directly. Don't know. I think you need everything gromacs related that comes out. Do it in an empty directory. Thank you for replying! yorquant 2012/11/1 David van der Spoel On 2012-10-31 16:31, Yorquant Wang wrote: Hi GMX-users, Klauda et al (J. Phys. Chem. B, 2012, 116 (

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

cript 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.

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

ed in OPLS/AA, 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 -- Dav

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., Upp

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

romacs.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 -- gmx

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

ghtly more 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 maili

Re: [gmx-users] average velocity

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.se

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)

e 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: +46184714205. sp...@

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

ity 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 &

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)

o 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://fol

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.se

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