Re: [gmx-users] Proper 1-octanol box preparation

://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., Professor of Biology Dept

[gmx-users] BAR gives different result than TI

-10.8 -17.9 DEE -11.0 -1.8 -7.4 Since for NBA the results are pretty close it seems that the protocol should be right, and the numbers seem to have converged pretty good as well. Any clues why these results could be so different? -- David van der Spoel, Ph.D., Professor of Biology

Re: [gmx-users] Does thole polarization work?

in the gas phase and report back (off-list) 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. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users

Re: [gmx-users] Question about the translational diffusion

On 2012-07-05 16:23, sa wrote: Hi all, : A quick question here: Does the g_msd program (v4.5.5) take into account the finite size effect due to PBC when it computes/gives translational diffusion ? sa yes. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol

Re: [gmx-users] Re: Re: g_sham problem

that this is complicated too, because the volume of the bins in your 2D plot are not the same in general, so even if you have more points in one bin then in another it might be because the volume is larger, rather than that it is more populated. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell

Re: [gmx-users] More accurate potential energy in output?

-- 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] Topology file

not compare directly in this way, since different force field may have different number of e.g. dihedral terms. Never use the gmx force field by the way. Thanks in advance . Sincerely, Shima -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box

Re: [gmx-users] g_sgangle problem

defining the one p atom and 1 n atom then there was no problem should i define all the index file to 2 group part and then average from the rezult or should i do something in index file that can solve the problem best regards yousef nademi g_sgangle -h. Please read carefully. -- David van der

Re: [gmx-users] Thole polarization between different molecules

/Thole-polarization-between-different-molecules-tp428.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] Topology file for simulation of inorganic compounds

consult the following page and be prepared for a significant time investment: http://www.gromacs.org/Documentation/How-tos/Parameterization -Justin Hm, that page is slightly outdated. You want to google for antechamber / gaff /amber respectively charmm / cgenff -- David van der Spoel, Ph.D

Re: [gmx-users] PLUMED-GROMACS force constant, angle unit

in degree unit ? Thanks Tarak -- 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

[gmx-users] BAR / g_bar problems

://folding.bmc.uu.se/images/koko.jpg Molecule Energy Exper Methanol -8-21 Ethanol -9-21 Diethylether -11-7 Neopentane -10 +11 any clue? -- 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] Force fields, is there a review article?

in this topics). maybe someone else in the ML can be more helpful than me about this. We have done a couple of evaluations recently Erik Marklund, Daniel Larsson, Alexandra Patriksson, David van der Spoel Carl Caleman: Structural stability of electrosprayed proteins: temperature and hydration

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

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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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 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] 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 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] 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] 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] 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] 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] 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] 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] 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

[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

[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

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

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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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

[gmx-users] FEP instability

-lambda = 0 init-lambda = 0.1 couple-lambda0 = vdw couple-lambda1 = vdw-q free-energy = yes I've also tried using sc-alpha = 0 sc-power = 0 Any clues what could go wrong? Could it be due to the virtual sites? -- David van der Spoel, Ph.D., Professor of Biology Dept

Re: [gmx-users] Shell MD

be highly appreciated. * *Thanks a lot. * ** *Liyan * -- 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] g_wham and entropic subtraction

If it does not say so explicitly (and it does not when using g_wham -h) it does not. -- 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] How DispCorr influsnces pressure

. The statistics is a few nanoseconds, so this cannot be just a result of large fluctuations. Thanks in advance. Dispcorr is only for homogeneous liquids. It should not be used for membranes. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596

Re: [gmx-users] Poor exchange probability for REMD

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. Box 596

Re: [gmx-users] Using tables to construct a z-dependent 12-3 potential

University '12 AB Chemistry -- 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] to gro or not to gro

://utoronto.ca:* It's more useful if you provide more information. What was the .pdb file (can I download it from the pdb databank?) was there water? what version of gromacs? was it compiled in double or single precision? what were your mdp parameters? -- David van der Spoel, Ph.D., Professor

Re: [gmx-users] to gro or not to gro

-- 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] g_clustsize

. Please help me. Best Regards SARA -- 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] to gro or not to gro

On 2011-11-26 20:15, Igor Druz wrote: On Sat, Nov 26, 2011 at 6:37 PM, David van der Spoel sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se wrote: On 2011-11-26 19:07, Igor Druz wrote: On Sat, Nov 26, 2011 at 5:35 PM, chris.ne...@utoronto.ca mailto:chris.ne...@utoronto.ca

Re: [gmx-users] Using tables to construct a z-dependent 12-3 potential

though... If all else fail grep for wall in the source code :). Thank you so much! Olivia On Sat, Nov 26, 2011 at 10:13 AM, David van der Spoel sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se wrote: On 2011-11-26 15:58, Olivia Waring wrote: Hello all, I'm wondering

Re: [gmx-users] to gro or not to gro

)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto: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

Re: [gmx-users] g_rdf -com

you first have to define which surfactants belong together before g_rdf can do this - make an appropriate index file, maybe g_clustsize can help. -- 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] to gro or not to gro

in pdb2gmx, editconf, trjconv is a good idea. We should not make *any* presumptions about what the user wants to do (although it is hard). I've created redmine issue 846 to remind us of this problem. http://redmine.gromacs.org/issues/846 -- David van der Spoel, Ph.D., Professor of Biology Dept

Re: [gmx-users] Re: gmx-users Dipole

. David van der Spoel, PhD, Professor of Biology Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se

Re: [gmx-users] .top to .itp file conversion

. Is there any command in gromacs or any other tool to do so. Thanks Neeru Sharma CDAC,Pune (India) emacs or vi. your choice. -- 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] gas-phase protein simulation

yes all cutoffs 0 and epsilon_rf 1 and nstlist 0 as well. Toodle pip! On Nov 30, 2011, at 8:39 PM, Shi, Huilin huil...@imail.iu.edu wrote: Hi, I would like to run a gas-phase protein simulation (with charge state of +8). I have read this paper : Biochemistry, 2007, 47, 933-945. In

[gmx-users] postdoctoral vacancy in computational biochemistry/biophysics

=Vacancies To apply, send a CV, publications list, brief overview of research interests and contact details of three people who can provide letters of recommendation directly to Lynn Kamerlin at kamerlin[at]icm.uu.se -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol

Re: [gmx-users] diffusion coefficient

with a workflow derived from the information here http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions Mark -- 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] diffusion coefficient: apparently, g_msd messes up the MSD due to PBC

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. David van der Spoel, PhD, Professor of Biology Dept. of Cell and Molecular

Re: [gmx-users] g_hbond

29.376 12.907 Relaxation 0.063 15.803 11.370 Thankyou for any help, Dr. M. S. Sulatha Dept. of Chemical Engineering IIT-Madras India -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden

Re: [gmx-users] g_hbond

0.034 29.376 12.907 Relaxation 0.063 15.803 11.370 Thankyou for any help, Dr. M. S. Sulatha Dept. of Chemical Engineering IIT-Madras India -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala

Re: [gmx-users] regarding x2top error

for 41 out of 42 atoms.* i dono how to resolve this . can anyone pls tell me how to solve tis. i checked my .n2t file also. but i couldnt get the error. help me with your answer ... thanking you, -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala

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