Re: [gmx-users] Replicating an experiment

your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK Malaysia legislation. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596

Re: [gmx-users] Replicating an experiment

going into the wrong phase. Thanks very much indeed!! From: gmx-users-boun...@gromacs.org on behalf of David van der Spoel Sent: Sat 12/25/2010 10:28 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Replicating an experiment On 2010-12-25

Re: [gmx-users] Reg: Simulating large number of molecules

with required box dimensions. So how one can about simulating more than 1000 molecules of alkanes r any molecules for that matter? I know that this problem doesn.t occur for water. any help is highly appreciated. Regards Vinoth genbox is memory hungry. Try using genconf. -- David van der Spoel, Ph.D

Re: [gmx-users] Nose-hoover T-coupling in REMD

am not sure whether it will introduce some artifacts in the simulation and what kind of artifacts. Could you tell me? Thanks in advance. Best, Qin -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala

Re: [gmx-users] Nose-hoover T-coupling in REMD

On 2010-12-24 13.15, ms wrote: On 24/12/10 10:36, David van der Spoel wrote: On 2010-12-24 11.04, Mark Abraham wrote: On 22/12/2010 5:44 PM, Qin Qiao wrote: Dear all, I posted yesterday but didn't get answer..I guess it's due to my wrong approach to ask. I would like to explain more and hope

Re: [gmx-users] Nose-hoover T-coupling in REMD

On 12/24/10 6:40 PM, ms wrote: On 24/12/10 12:26, David van der Spoel wrote: I'm not an expert, but isn't Berendsen usually not used because it doesn't give a correct ensemble? I may be partial because I personally know Giovanni Bussi, but it seems from what I've heard that v-rescale

Re: [gmx-users] PME or Reaction field suitable for Gromos forcefield ?

any artifact if used with Gromos forcefield ? Alternatively, if I can get a sample .mdp file for typical gromos forcefield simulation, that will also be very helpful . Sanku Check out Oliver Lange, David van der Spoel and Bert de Groot: Scrutinizing Molecular Mechanics Force Fields

Re: [gmx-users] PME or Reaction field suitable for Gromos forcefield ?

= 0 ; EWALD/PME/PPPM parameters pme_order= 6 ewald_rtol = 1e-6 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = no *From:* David van der Spoel sp

Re: [gmx-users] Forces in source code

source code for this task. Could you help me and give me any advices? - in what .c files are forces and pull force are evaluated? Or from what I must start? Best regards, Petr. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124

Re: [gmx-users] water-air interface surface tension

/007525G0/163mail_guide.html?id=2716 -- 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] Re: correlation function

. If you have memory problems the simplest solution is to either buy more memory or to split the calculation over molecules. -- 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] tpbconv -zeroq results all coulombic energies to zero

is the correct way to zeroize the charge for a group of atoms? Thanks, Bin -- 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] Thermostating in NEMD

-- 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] protein folding

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., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp

Re: [gmx-users] How to obtain the coordinates of atom 100 with number in the frame 100 using xdrfile in C code

. Yours sincerely, Chaofu Wu, Dr. You just have to read a whole frame and extract the coordinate that you want. -- 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] Gromacs Quotes

On 2010-11-18 20.48, Sikandar Mashayak wrote: Hi I am wondering where can I find the file containing all the Gromacs Quotes , which are printed at the end of program run? thanks sikandar share/gromacs/top/gurgle.dat -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec

Re: [gmx-users] Re: g_hbond modification

. Underwood Chemistry Department 560 Oval Drive West Lafayette, IN 47907 -- 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] Reg: NPT Equilibration of water

/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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- David van der Spoel, Ph.D

[gmx-users] Fwd: -pbc nojump

I did simulation of protein-dna complex in water solvent. After simulation, two strands of dna was separated when I displayed my a.xtc with VMD.I used (trjconv –f a.xtc –s a.tpr –n a.ndx –o b.xtc –pbc nojump) and problem fixed. But now I have another problem. Before using –pbc nojump, there

Re: [gmx-users] Fwd: -pbc nojump

On 2010-10-27 09.40, David van der Spoel wrote: I did simulation of protein-dna complex in water solvent. After simulation, two strands of dna was separated when I displayed my a.xtc with VMD.I used (trjconv –f a.xtc –s a.tpr –n a.ndx –o b.xtc –pbc nojump) and problem fixed. But now I have

Re: [gmx-users] Job crash: checkpoint file

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: +46184714205. sp

Re: [gmx-users] g_dipole ? =salt-molecule = Does Gromacs consider counter ions?

will not consider counter ions to calculate the dipole moment ??? Thank you Lin you should try to understand what is going on yourself rather than sending many email to the mailing list. Please read the source code of the program. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec

Re: [gmx-users] RE: Gibbs free energy of binding

as E2 as bound system . what does (E1-E2)mean? I think it is binding free energy,Is not it? in the other hand when we are working on NPT ensamble it means Gibbs free energy is the main energy and our total energy is equal to Gibbs free energy. Then,what is the problem? -- David van der Spoel

Re: [gmx-users] g_dipole ? = what is the bond length of the ionic bond in the dipole moment calculation?

will subtract their charge at their center of mass ? -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20101019/4cf32833/attachment.html -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec

Re: [gmx-users] g_dipole ? = dipole moment ?

that the molecule becomes as big as the box. What does will subtract their charge at their center of mass this mean? Why will subtract their charge at their center of mass ? -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box

Re: [gmx-users] Point Dipoles

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: +46184714205. sp

Re: [gmx-users] g_dipole ? = dipole moment ?

Dipole moment (Debye) - Average = 32.1161 Std. Dev. = 2.9926 Error = 0.0095 -- 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] Simulation parameter problem about protein unfolding

! -- 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] g_dipole ? = dipole moment ?

2.000 Average volume over run is 221.043 Dipole moment (Debye) - Average = 32.1161 Std. Dev. = 2.9926 Error = 0.0095 -- 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] Extracting potential energy of protein units

On 2010-10-14 21.51, Jyoti Mahalik wrote: Using g_energy I can extract the energy of the whole system. But I want to extract the energy (potential energy) of the protein units in my system. Is it possible to do it in GROMACS or any other application? How would you define that? -- David van der

Re: [gmx-users] why does trjcat take so much memory?

. Sure, I could find a larger memory system, but why does it take =3x more memory than the individual files took in disk space? Does anybody know any commands This is gromacs 4.0.5 and 4.0.7 and 4.5-beta2. Thank you, Chris. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec

Re: [gmx-users] Gromacs installation problem @ RHEL5.5 server

posting! Please don't post (un)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 -- -- Regards, N. Sathishkumar, -- David van der

Re: [gmx-users] REMD speed calculation compared to classical MD

)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. David van der Spoel, PhD, Professor of Biology Dept

Re: [gmx-users] free energy decomposition

the PMF by unbiasing the umbrella potential. Sanku -- David. David van der Spoel, PhD, Professor of Biology Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone

Re: [gmx-users] Re: swiss param query

Molecular Modeling Group Swiss Institute of Bioinformatics CH-1015 Lausanne Switzerland http://lausanne.isb-sib.ch/~mcuendet/ == -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596

Re: [gmx-users] Gromacs benchmarking results

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, 75124

[gmx-users] Re: pdb2gmx problem

be angry with me. -- Ahmet YILDIRIM -- 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 calculation_2

9909 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. -- 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] viscosity calculation

the output .xvg; you will find it should contain two quantities: bulk and shear viscosity. -Justin Regards, Payman -- 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: Problem with pressure coupling

= berendsen Pcoupltype = isotropic tau_p= 1 compressibility = 4.5e-5 ref_p= 1.0 ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel = no ; OPTIONS FOR BONDS constraints = none -- David van der

Re: [gmx-users] viscosity calculation_2

Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of David van der Spoel Sent: September 29, 2010 1:03 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] viscosity calculation On 2010-09-29 20.52, Payman Pirzadeh wrote: Well, two questions

Re: [gmx-users] Reg: Liquid-liquid interface simulation

-liquid interface simulation. Regards Vinoth We prefer to keep discussions on the mailing list for more direct impact and for archiving purposes. If there are tutorials or howtos on certain topics they can be uploaded to the website. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell

Re: [gmx-users] LJ potential

On 2010-09-27 18.37, nishap.pa...@utoronto.ca wrote: Hello, Is there a way to turn off the 6-term in LJ 6-12 potential? -Nisha P. Set the parameters to zero? -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden

Re: [gmx-users] data.xvg for g_kinetics ?

. In principle, you should be able to use other metrics like R(g), native contacts, etc. That's correct, and the RMSD is quantized by setting the cut-off value. -Justin thanks a lot Kevin -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596

Re: [gmx-users] Re: rotational correlation function

? Is trjconv the solution again? No and no. Maybe when you use the -debug option to trjconv it spits out the rotation matrix but I'm not sure. Anyway you need to start trying things out from here. regards, Paymon On Thu, 2010-09-23 at 20:40 +0200, David van der Spoel wrote: On 2010-09

Re: [gmx-users] Re: rotational correlation function

) for rotational velocoty to make sense. -- Dr. Vitaly V. Chaban Department of Chemistry University of Rochester Rochester, NY 14627-0216 United States of America -- 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] Re: rotational correlation function

simulation study}, journal = {J. Chem. Theory Comput.}, volume = {2}, year= {2006}, pages = {1228-1236}, } Sorry for mass of questions. Regards, Paymon On Thu, 2010-09-23 at 08:20 +0200, David van der Spoel wrote: On 2010-09-23 01.27, Paymon Pirzadeh wrote: Dear Dr. Chaban, I

Re: [gmx-users] Re: rotational correlation function

On 2010-09-23 20.38, Paymon Pirzadeh wrote: Great tips and advices. I appreciate your attention. But, what would the g_rms -fit rot+trans do? compute the rmsd. something different. I said trjconv. Paymon On Thu, 2010-09-23 at 20:07 +0200, David van der Spoel wrote: On 2010-09-23 18.14

Re: [gmx-users] Urea-water

of repulsion but is that correct? Did you look at the graph? Please do, then you will understand. I would appreciate some help. Thanks. -Nisha P -- 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_hbond

. 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

[gmx-users] Re: Dear Dr.Van Der Spoel

- yet. Algorithms are being implemented for allowing that, but that will take until version 5.0. Please ask questions on the gmx-users mailing list. -- 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] reg grompp error in QM/MM of mopac gromacs

, line: 99 Fatal error: Invalid pairs type 0 --- the suggestions are highly appericiated -- 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] Convert LJ 9-6 to LJ 12-6?

direction to a paper, bit of code etc. g_sigeps -h Changing the source code of the other program to read in LJ 9-6 is something I'd rather avoid if there is another solution. Thanks -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box

Re: [gmx-users] RDF converge to zero than 1, why?

/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] RDF converge to zero than 1, why?

, that should converge to the number of particles. See manual. Rob Quoting David van der Spoel sp...@xray.bmc.uu.se: On 2010-09-15 20.34, tekle...@ualberta.ca wrote: Dear Justine, Then my guess is you don't have a PBC problem, but perhaps a convergence problem. You're only analyzing 1 ns of data; I

Re: [gmx-users] xpm2ps failure - memory allocation

memory Version 4.0.7 produces the correct output from the same input files (.xpm and .m2p). Any ideas? -Justin Please submit a bugzilla, don't forget to specify the machine used, since this kind of message is very much dependent on the libc version. -- David van der Spoel, Ph.D., Professor

Re: [gmx-users] Regular vs. CHARMM TIP3P water model

= 0 optimize_fft = yes ; RUN CONTROL PARAMETERS integrator = md dt = 0.002 nsteps = 20 comm_mode= Linear nstcomm = 1 comm_grps= System -- David van der Spoel, Ph.D

Re: [gmx-users] Problem Installing 4.5.1

appreciated. Thanks in advance. There is an error in the demo script. Please move on to the next part of the tutorial. We'll fix it for the next point release. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden

Re: [gmx-users] Polyglycine PDB file.

be straightforward with text editors. -- 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: Polyglycine PDB file.

into ATOM maintaining the spacing it should 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] pdb2gmx gmx 4.5: issues with atom name in last column

://www.bio.cam.ac.uk/~awd28 -- 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] Replica exchange with multiple tables?

)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/mailing_lists/users.php -- Quaerendo Invenietis-Seek and you shall discover. -- David van der Spoel, Ph.D

Re: [gmx-users] Multiple nrexcl commands in GROMACS

, NY 12180 You can simply generate the exclusions yourself and specify them per molecule [ exclusions ] ; From To... 1 2 3 4 2 1 3 4 and so on. -- 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_order question

is for water molecules though. Also, does it calculate an average value or give a profile as a function of time? thanks, Paymon Have you tried it? You can compute tetrahedrality for water, and also do it in slices accross the box axis. It computes the average over time. -- David van der Spoel, Ph.D

Re: [gmx-users] g_order question

at 20:37 +0200, David van der Spoel wrote: On 2010-08-31 20.26, Paymon Pirzadeh wrote: Hello, It is said in the mannual that g_order compute the order parameter per atom for carbon tails. Can it also calculate order (degree of tetrahedrality) for water molecules if only water oxygens are selected

Re: [gmx-users] g_order question

-Sgsl sg-ang-slice.xvg Output, Opt. xvgr/xmgr file -Sksl sk-dist-slice.xvg Output, Opt. xvgr/xmgr file On Tue, 2010-08-31 at 21:15 +0200, David van der Spoel wrote: On 2010-08-31 21.10, Paymon Pirzadeh wrote: Yes, I tried it, but I run into segmentation fault. Here is part of the error

Re: [gmx-users] VDWradii.dat

of 1.6652A, I am not sure where that value came from. I would really appreciate some help! Thanks. -Nisha P Did you get the pqr file from editconf? Then read editconf -h. Check the -sig56 option. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala

Re: [gmx-users] drude oscillator with thole polarization

Messaging Program. -- 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] dipole moment of molecule of trans and cis azobenzene ?

more hydrophobic than the cis-one? = how can I calculate the dipole moment from the given partial charges for each atom? mu = sum_i q r Or g_dipoles. Thank you Lin -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala

Re: [gmx-users] VDW radii of Br and K+

79.90400-1.000 A4.62376e-01 3.76560e-01 opls_408 K+ 19 39.09830 1.000 A4.93463e-01 1.37235e-03 You see that K+ has larger sigma than Br-. Thanks. -Nisha P -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596

Re: [gmx-users] Epsilon AA, Epsilon AB, Epsilon BB

. [ nonbond_params] ; i j type c6 c12 O O 1 1 1 N N 1 0.5 0.5 O N 1 1.5 1.5 whatever -- David. David van der Spoel, PhD, Professor of Biology Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124

Re: [gmx-users] GB Parameters

the current Charmm implementation although there are rumours that parameters exist. -- 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] please, how edr data is xdr packed?

very silly. Many thanks in advance, Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- David van der Spoel, Ph.D., Professor of Biology Dept

Re: [gmx-users] Does anyone know how to get the file charmm_gromacs.tar.gz?

. It contains the charmm ff. -- 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] Calculate observed Acceptance Ratio from REMD simulation

664 684 667 692 659 627 699 688 699 683 ... Repl average number of exchanges: Repl 0123456789 10 ... Repl .55 .56 .55 .57 .54 .52 .58 .57 .58 .56 ... -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell

Re: [gmx-users] installation problem of gromacs binary

is unaware of anything you've done outside RPM. Either install a *single-precision* FFTW3 RPM, or GROMACS also from source. Mark And, obviously, you might want to consider a newer gromacs version. For quite a few distributions you can use yum or apt-get gromacs. -- David van der Spoel, Ph.D., Professor

Re: [gmx-users] pdb2gmx-4.5 treats DNA as protein (and fails)

for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- -- 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] pdb2gmx-4.5 treats DNA as protein (and fails)

On 2010-08-16 14.44, Maiki wrote: David van der Spoel wrote: On 2010-08-16 12.34, Maiki wrote: So, anybody knows why it does that or how to deal with nucleic acids? I only saw one similar question asked recently (with different error) which was also left without answer. Not all force fields

Re: [gmx-users] g_gyrate -p = the radii of gyration about the principal axes ?

to be a constant factor. Gromacs computes sqrt (sum m (r-r_com)^2 / sum m) I'm pretty sure it says so in the manual. Thank you Lin -- 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] g_gyrate -p = the radii of gyration about the principal axes ?

is the definition of the radii of gyration about the principal axes ? i have checked the Gromacs manual but see nothing there. The difference seems to be a constant factor. Gromacs computes sqrt (sum m (r-r_com)^2 / sum m) I'm pretty sure it says so in the manual. Thank you Lin -- David van

Re: [gmx-users] RDF

of Basic Sciences Azerbaijan University of Tarbiat Moallem. -- 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

Re: [gmx-users] Protonate error

file. -- *Best Regards, * B. Sarath Kumar, M.S (By Research), Centre for Biotechnology, Anna University, Chennai. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp

[gmx-users] Another test

This time from gmail. David. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it

[gmx-users] Test

Hi, this is a test to see whether the mailing list works. Cheers, -- 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] Hi

. -- 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] new beta release - gromacs-4.5-beta2

-- 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: Question

Please let me know the answer of this question: I can't understand it. How can this occur?(You had mentioned it in the Gromacs manual user guide(chapter 7)) Can gromacs write* conserved energy quantity* in log file when we are simulating a *NVT* ensemble? Do you mean* Kinetic energy* is

Re: [gmx-users] Problem in Replica Exchange

frequency of exchange do you use? Please give mdrun command line -- 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

Re: [gmx-users] Problem in Replica Exchange

-machinefile $PWD/machines \ /share/apps/gromacs-4.0.5/bin/mdrun_mpi \ -s topol_.tpr -multi 8 -pd replex 100 Thanks, Nimesh On Tue, Aug 3, 2010 at 10:11 AM, David van der Spoel sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se wrote: On 2010-08-03 17.08

Re: [gmx-users] RDF

. It is normalized such that in a condensed system the number density goes to 1. The total number density is part of the equation, as described in the manual (8.2). -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden

Re: [gmx-users] GROMACS-4.5-beta1 is out!

or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- 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 visualise protein conformation after every 1ns

file. Thanks -- Sonali Dhindwal trjconv -o koko.pdb -dt 1000 -s -f -sep -- David. David van der Spoel, PhD, Professor of Biology Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596

Re: [gmx-users] Phonon calculations in periodic crystals

Kelley Anne Myers Kelley Professor of Chemistry, School of Natural Sciences Secretary-Treasurer, APS Division of Laser Science University of California, Merced 5200 North Lake Road, Merced, CA 95343 Tel. 209-228-4345 amkel...@ucmerced.edu http://faculty.ucmerced.edu/amkelley/ -- David van der

Re: [gmx-users] Pressure coupling

-Seek and you shall discover. -- 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] (no subject)

, and then rename them in a text editor and throw away superfluous atoms. -- David. David van der Spoel, PhD, Professor of Biology Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124

Re: [gmx-users] grompp errors

. This new error is my attempt to fix this error. Sincerely, ~Amanda Watkins SBC 2012 -- David. David van der Spoel, PhD, Professor of Biology Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596

Re: [gmx-users] Re: the Pressure control in GROMACS 4.0.7

Associate Researcher -- 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] Re: Pressure control in GROMACS 4.0.7

small. Whether the average is 1 or 5 does not make a difference if the fluctuation are two orders of magnitude larger. -- 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: the Pressure control in GROMACS 4.0.7

999.61 1776.868286 999.200073 55.826385 999.400024 538.847107 999.600037 4052.162842 999.800049 -6294.055664 1000.61 -1811.536377 Thanks! Zhongjin He -- 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_principal: memory corruption

.gro file was selected for -f flag, but failed even for a shorter trajectory file. What is the way around for this problem Thank you in advance! Please submit a bugzilla with a short trajectory (since it crashes at time 0 one frame is enough). -- David van der Spoel, Ph.D., Professor

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