Re: [gmx-users] Free volume variation during the simulation

Wed, May 6, 2020 at 08:23 David van der Spoel wrote: Den 2020-05-06 kl. 01:13, skrev Mohamed Abdelaal: Hello everybody, I have two fundamental questions please. I have measured the fee volume and I discovered that, the free volume changes with respect to the time during the production run

Re: [gmx-users] Free volume variation during the simulation

t change. Many Thanks, Mohamed This is due to atomic fluctuations, that is they overlap more or less depending on their distance, Did you use the freevolume tool in gromacs? It may also depend on whether each freevolume calculations is converged (-ninsert option). -- David van der Spoel, Ph.D

Re: [gmx-users] Trouble with restrained dihedrals

etrovic Educator Computational Science and Technology School of Electrical Engineering and Computer Science KTH Royal Institute of Technology -- David van der Spoel, Ph.D., Professor of Biology Uppsala University. http://virtualchemistry.org -- Gromacs Users mailing list * Plea

Re: [gmx-users] Problem force constant bond stretc.

advance for your help. Vbond = (k/2) (r - r0)^2 Some methods do not use the division by two, so it can be a matter of definition. -- David van der Spoel, Ph.D., Professor of Biology Uppsala University. http://virtualchemistry.org -- Gromacs Users mailing list * Please search the archive at http

Re: [gmx-users] (NEW USER) Determining Complex Dielectric property of a solid state system

ease report back when you have, this is a bit tricky business though. You may check my old paper, however it is not entirely correct since trying to extract the dielectric constant at infinite frequency from a non-polarizable ff is not possible. https://aip.scitation.org/doi/abs/10.1063/1.476482

Re: [gmx-users] Can we implement NMR restraint data in Gromacs?

case. -- David van der Spoel, Ph.D., Professor of Biology Uppsala University. http://virtualchemistry.org -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Su

Re: [gmx-users] Post processing REMD simulation

help analyzing that if it still works. Many thanks On Sun, Apr 12, 2020 at 2:25 AM David van der Spoel wrote: *Message sent from a system outside of UConn.* Den 2020-04-12 kl. 05:40, skrev Mohammad Madani: Dear all, Hi. I have problems about the analysis of the REMD simulation. I run the rem

Re: [gmx-users] Post processing REMD simulation

instance. Many thanks. Mohammad -- David van der Spoel, Ph.D., Professor of Biology Uppsala University. http://virtualchemistry.org -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

Re: [gmx-users] Problem with pdb2gmx

n the topology, I got this warning message : Warning:long-bond... I don't know what should I do to retain the covalent bond. I will appreciate it if you help me with this problem. -- David van der Spoel, Ph.D., Professor of Biology Uppsala University. http://virtualchemistry.org -- Gromacs Use

Re: [gmx-users] How to use GROMACS license?

. -- David van der Spoel, Ph.D., Professor of Biology Uppsala University. http://virtualchemistry.org -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Su

Re: [gmx-users] Onsager coefficient

h two subscripts. Otherwise it looks a bit like Einsteins formula. On Tue, 31 Mar 2020 at 09:59, David van der Spoel wrote: Den 2020-03-30 kl. 22:51, skrev Sina Omrani: Hi dear Gromacs users, Sorry to ask again but I really appreciate the help on this subject. thanks. On Fri, 27 Mar 2020 at

Re: [gmx-users] Onsager coefficient

only been studied by simulation for simple Lennard-Jones particles.59". But maybe this is not relevant at all. On Tue, 31 Mar 2020 at 17:51, David van der Spoel wrote: Den 2020-03-31 kl. 14:11, skrev Sina Omrani: As far as I know, the Onsager coefficient is used to calculate MS diffusi

Re: [gmx-users] Onsager coefficient

mean? And for my curiosity, what kind of macroscopic properties are you after? As far as I know many if not most macroscopic properties can be computed directly from a simulation, but I may be wrong. On Tue, 31 Mar 2020 at 11:05, David van der Spoel wrote: Den 2020-03-31 kl. 08:17, skrev

Re: [gmx-users] Onsager coefficient

monash.edu - When the only tool you own is a hammer, every problem begins to resemble a nail. On Tue, 31 Mar 2020 at 16:28, David van der Spoel wrote: Den 2020-03-30 kl. 22:51, skrev Sina Omrani: Hi dear Gromacs users, Sorry to ask again but I really appreciate t

Re: [gmx-users] Onsager coefficient

oogle does not help either. What is an Onsager coefficient? -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se -- Gromacs Users mailing list * Ple

Re: [gmx-users] Thin film drifting

Den 2020-03-29 kl. 22:46, skrev Alex: On Sun, Mar 29, 2020 at 2:49 PM David van der Spoel wrote: Den 2020-03-29 kl. 19:43, skrev Alex: Thanks. On Sun, Mar 29, 2020 at 11:59 AM David van der Spoel < sp...@xray.bmc.uu.se> wrote: Den 2020-03-29 kl. 15:16, skrev Alex: Thank Prof. v

Re: [gmx-users] Thin film drifting

Den 2020-03-29 kl. 19:43, skrev Alex: Thanks. On Sun, Mar 29, 2020 at 11:59 AM David van der Spoel wrote: Den 2020-03-29 kl. 15:16, skrev Alex: Thank Prof. van der Spoel for the response. No, it isn't. The thin film is solid. There are interaction within the thin film and with wat

Re: [gmx-users] Thin film drifting

n Sun, Mar 29, 2020 at 2:44 AM David van der Spoel wrote: Den 2020-03-29 kl. 05:24, skrev Alex: Dear all, In a system, I have a thin_film (infinitive in x-y directions) with water on top and bottom of it, PBC = xyz. By the below flags I try to remove the motion of the center of mass of the two

Re: [gmx-users] Thin film drifting

film should prevent this, hav eyou tried turning off comm? Historically this has been a fix for the Berendsen thermostat that accumulates energy, however with a stochastic thermostat it should not be necessary. Not sure about Nose-Hoover though. -- David van der Spoel, Ph.D., Professor of

Re: [gmx-users] Per atom energies

www.mdstress.org -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se -- Gromacs Users mailing list * Please search the archive at http://www

Re: [gmx-users] gmx msd unusual unit

from time 1000 to 9000 ps # D[   UNK] = 0.0031 (+/- 0.0004) (1e-5 cm^2/s) Thank you Joe -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se -- Gr

Re: [gmx-users] positive potential energy

Sent from Yahoo Mail on Android No. I just answered a similar question. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se -- Gromacs Users mailing

Re: [gmx-users] potential energy doesn't have negative value

subtract 100 times the energy of the monomer, then you will have the enthalpy of vaporization (+/- kT) which you can compare to experiment. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. P

Re: [gmx-users] Setting a electric field in a simulation

u get? -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.or

Re: [gmx-users] Troubleshooting Generic Floating Point Exception Errors

Ph.D. INSPIRE Postdoctoral Fellow Gormley Lab, Rutgers University These are rather uncommon unless you have truly unphysical setups (e.g. due to a unit problem) or broken hardware. Hard to tell based on your mail unfortunately. -- David van der Spoel, Ph.D., Professor of Biology Head of Department,

Re: [gmx-users] Gromacs 2020 fails to run adh_cubic_vsites

Tieleman Jon Vincent Teemu Virolainen Christian WennbergMaarten Wolf Artem Zhmurov and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel Copyright (c) 1991-2000, University of Groningen, The Netherlands

Re: [gmx-users] Can't observe ion separation under the influence of electric field

though. The force on the atoms will be quite small still compared to interatomic forces therefore the effect may be limited. F = q E (convert to right units). In GROMACS MD units a typical interatomic force is ~ 1000 kJ/mol/nm^2. Thank you, -- David van der Spoel, Ph.D., Professor of

Re: [gmx-users] Estimation of configurational entropy

-- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Ma

Re: [gmx-users] Gromacs question

, Daniel *Daniel Kneller* Postdoctoral Research Associate Neutron Scattering Division Neutron Sciences Directorate Oak Ridge National Laboratory -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Upp

Re: [gmx-users] What is the difference between density of states (gmx dos) and vibrational power spectrum (gmx velacc -os)?

e National Laboratory -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se -- Gromacs Users mailing list * Please search the archive at http://www.groma

Re: [gmx-users] Regarding calculation of configurational entropy

at is going on here and if I made mistakes then what it is? Thank You Amit Kumar Did you use double precision? This is needed to get sufficient accuracy, -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-7512

Re: [gmx-users] How to add osmotic stress

Den 2020-02-02 kl. 17:46, skrev Alex Mathew: How to introduce osmotic stress on a simulation system to study the transportation differences in varying conditions.( protein-membrane system) Use a double membrane and different concentrations in the water phases. -- David van der Spoel, Ph.D

Re: [gmx-users] Dipole moment and dielectric constant - gmx dipoles

s are larger than gmx dipoles, I wanted to ask that there is something gmx dipoles is using in order to calculate the and , causing this difference? I appreciate any help in this regard. Best regards, Iman -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molec

Re: [gmx-users] .dat file from gmx densmap doestnottmatchtprescribedtsize

https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +4618471420

Re: [gmx-users] lifetime of hydrogen bond

-- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mai

Re: [gmx-users] Force (%)" value in md.log file

Total139.440 4729.873 100.0 " I am comparing with a published benchmark having values for "*Force= 14.9%".* -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. P

Re: [gmx-users] Young's modulus

compressibility, see e.g. Eqn 11 in J. Chem. Theor. Comput. 8 pp. 61-74 (2012) This can likely be extended to solids as well. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. P

Re: [gmx-users] rotacf error

Proline residues in your protein which do not have a H. More tricky, if you have two prolines you get an even number of atoms again but it can be completely wrong. Solution is to remove prolines in make_ndx before you select a group of NH. -- David van der Spoel, Ph.D., Professor of Biology Head of

Re: [gmx-users] Generalized Born solvation

this in error please contact the sender immediately by return electronic transmission and then immediately delete this transmission including all attachments without copying, distributing or disclosing the same. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell

Re: [gmx-users] Lipidbook webpage is off - is it possible to find its content somewhere?

ne: +1 (480) 727-9765 FAX: +1 (480) 965-4669 Department of Physics: https://physics.asu.edu/content/oliver-beckstein Center for Biological Physics: https://cbp.asu.edu/content/oliver-beckstein -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology,

Re: [gmx-users] solvent evaporation modeling

der Spoel: Proteins Structures under Electrospray Conditions Biochemistry 46 pp. 933-945 (2007) Yaofeng Wang, Daniel Larsson and David van der Spoel: Encapsulation of Myoglobin in a CTAB micelle - A Simulation Study Biochemistry 48 pp. 1006-1015 (2009) Erik Marklund, Daniel Larsson, Alexandra

Re: [gmx-users] toluene as a slovent

/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. End of gromacs.org_gmx-users Digest, Vol 188, Issue 3 ************* -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Up

Re: [gmx-users] Toluene .rtp

Here is simulation data for toluene http://virtualchemistry.org/molecule.php?filename=toluene.sdf and here are input files: http://virtualchemistry.org/ff.php -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Upp

Re: [gmx-users] anisotropic polarization

I apply it to my own molecules? Thank you for help. There is just one (rather obscure) anisotropically polarizable water model implemented. There is a topology called sw.itp, but there are better (isotropic) models out there. https://pubs.acs.org/doi/10.1021/jp003843l -- David van der Spoel, Ph.D.,

Re: [gmx-users] Vibrational frequencies from gromacs trajectory

ase a covariance analysis can be done. To get the pure frequencies it is better to use normal mode analysis. Please look these items up in the manual! -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsal

Re: [gmx-users] Regarding force field for silicon oxide

Den 2019-11-05 kl. 01:59, skrev Mijiddorj B: Dear Prof. David van der Spoel, Thank you very much for your reply and sending an amazing work. I am sorry for asking further questions. Can you give me an advice to use the parameters which were considered in the ref#44 in this work? Ref#44 uses the

Re: [gmx-users] cmake fails with custom gcc version

pperTarget: x86_64-pc-linux-gnu Configured with: ./configure --prefix=/home/mahmood/tools/gcc-6.1.0 --disable-multilib --enable-languages=c,c++Thread model: posix gcc version 6.1.0 (GCC) Any idea about that? Regards, Mahmood -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell

Re: [gmx-users] Regarding force field for silicon oxide

function that supports it and software to build topologies it works, e.g.: David van der Spoel, Erik J. W. Wensink and Alex C. Hoffmann: Lifting a glass from a wet table: a microscopic picture Langmuir 22 pp. 5666-5672 (2006) http://pubs.acs.org/cgi-bin/download.pl?la053284f/X8nx However please

Re: [gmx-users] Define intermolecular interactions in L-J simulation

system containing 500 A and 500 B, how can I apply this to the entire binary system. I was assumed that I can use atomtype instead of atom number? But how and where to specify that? Any suggestions? Thanks, Shi Use [ nonbonded_types ] A A 1 c6 c12 B B 1 c6 c12 A B 1 c6 c12 -- David van der

Re: [gmx-users] Frozen group moves!

0.554 0. 0. -0.5277 Anybody knows what might be the reason and how one can avoid that to happen? Regards, Alex Do you have pressure coupling turned on? Alternatively, are the frozen coordinates part of a compound that is constrained? Both of these could cause this. -- David van der

Re: [gmx-users] Normal Mode Analysis

al mode mdrun, it is giving an error on constraints. How do I solve this problem? Do I completely remove the constraints and then perform 'cg' minimization and 'nm' mdrun? Yes. Regards, Adip -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Mo

Re: [gmx-users] issues running virus capsid simulation

and it take many microseconds: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002502 https://pubs.acs.org/doi/abs/10.1021/ct3002128 -Justin -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box

Re: [gmx-users] Regarding obtaining potential energy using energy groups

upport/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala Univers

Re: [gmx-users] Batch mode error in GROMACS version 2019.2

cs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se -- Gromacs Users mailing list *

Re: [gmx-users] How to use gmx h2order when using four point water model

atom, and this command cannot output the correct results. Is there any solutions for this poblem? Thanks, Jun You can use trjconv to remove the virtual site from the trajectory, maybe it even works in the tool directly, without running trjconv. -- David van der Spoel, Ph.D., Professor of

Re: [gmx-users] pressure is coming 1.39

quests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205

Re: [gmx-users] How to Calculate tetrahedral order parameter

that case you would be better off computing free energies. Thanks and regards- Soham On Tue, 3 Sep 2019, 5:24 pm David van der Spoel, wrote: Den 2019-09-03 kl. 13:26, skrev Soham Sarkar: Dear all, I know this question was asked by many users before but searching them all I did

Re: [gmx-users] How to Calculate tetrahedral order parameter

? If gmx hydorder is the existing tool for calculating tetrahedral order parameter, went through this I did not understand the usage of it too. Thanks in advance- Soham What system, water? -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Upp

Re: [gmx-users] Question about Gromacs

time. Best Regards, Najla -- /*Kind Regards, */ /*Najla * / -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se -- Gromacs Users mailing list * Pl

Re: [gmx-users] Not all snapshots are written to trr during minimization

Grabarek Only writes when the energy goes down. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se -- Gromacs Users mailing list * Please search

Re: [gmx-users] Regarding too many LINCS warnings for bicarbonate ion

O3-H1 [ dihedrals ] ; impropers ; treated as propers in GROMACS to use correct AMBER analytical function ;i j k l func phase kd pn 1 3 2 4 1 180.00 4.60240 2 ; O1-O2- C1-O3 -- David van der Spoel, Ph.D., Pr

Re: [gmx-users] PRESS-XX, PRESS-YY, PRESS-ZZ in .edr file

? Are they principal pressures (stresses) averaged for all atoms during the simulation? What is the difference between those options and PRESSURE option? Thank you very much. Best, Anh Vo THe pressure is a tensor, see manual. -- David van der Spoel, Ph.D., Professor of Biology Head of Depar

Re: [gmx-users] Regarding OH, HH vector distribution

, 12:00 David van der Spoel wrote: Den 2019-07-31 kl. 06:12, skrev Omkar Singh: Thanks Sir, I did like that only, Now how can I make the distribution plot for these vectors. Eventhough I used "gmx analyze -f .xvg -dist .." command. But results is not proper. Can you suggest me rega

Re: [gmx-users] GROMOS 54a7 mapping warning

Larissa -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Sup

Re: [gmx-users] Regarding OH, HH vector distribution

gmx gangle -oh ? On Tue, Jul 30, 2019, 17:27 David van der Spoel wrote: Den 2019-07-30 kl. 07:55, skrev Omkar Singh: Hi, I did by "gmx gangle ..." command. But I am not getting good result, because I have a doubt in ndx file. Can you help me for making ndx file. How should I

Re: [gmx-users] Regarding OH, HH vector distribution

, assuming a three particle water model with atoms O H H. For HH it should be 2 3 5 6 8 9 etc. A simple script would do it. The dipole vector is somewhat harder. Thanks On Mon, Jul 29, 2019, 22:50 David van der Spoel wrote: Den 2019-07-29 kl. 18:26, skrev Omkar Singh: Hi, Meaning is that If

Re: [gmx-users] Regarding OH, HH vector distribution

question is clear. Probably. Check gmx gangle -g2 z Thanks On Mon, Jul 29, 2019, 16:33 David van der Spoel wrote: Den 2019-07-29 kl. 12:24, skrev Omkar Singh: Hello everyone, Is it possible that the probability distribution of HH, OH vector for bulk water is approximately linear? What do

Re: [gmx-users] Regarding OH, HH vector distribution

Den 2019-07-29 kl. 12:24, skrev Omkar Singh: Hello everyone, Is it possible that the probability distribution of HH, OH vector for bulk water is approximately linear? What do you mean? -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Upp

Re: [gmx-users] space dependent electric field

). To make things work quickly you can just hardcode the extra parameters you might need or abuse the existing one. Cheers, -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +4618471

Re: [gmx-users] Normal mode segmentation fault - memory problem ?

sing -end 82737 In that case the full matrix will be used. It may be slow though. Best, Marlon Sidore PhD - Post-doctoral fellow Institut d’Électronique et des Systèmes -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University

Re: [gmx-users] Specific heat calculations using gmx energy

enthalpy makes a sudden drop in the beginning of the simulation? If so this will influence the fluctuations a lot. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.

Re: [gmx-users] heat capacity collection

with an script)? thanks What kind of systems are these? I have quite a few reference data for liquids on http://virtualchemistry.org These were done using the gmx dos program that computes quantum corrections but this is not entirely trivial. -- David van der Spoel, Ph.D., Professor of Biology

Re: [gmx-users] Hydrogen bond autocorrelation

as the same H bond, unless you tell it not to with an option -nomerge. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se -- Gromacs Users mailing

Re: [gmx-users] Spectrum from nmeig command

have a summer worker implement proper calculation of intensities from next week. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se -- Gromacs User

Re: [gmx-users] High pressure variation during NPT equilibration of Protein-ligand system.

000 155.808731 89.002.646250 90.00 -284.466888 91.00 152.030930 92.00 280.804352 93.00 -182.475830 94.00 -268.784149 95.00 -470.018829 96.00 -163.642685 97.00 291.026855 98.00 -982.940430 99.000000 15

Re: [gmx-users] gmx_clustsize

is. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/

Re: [gmx-users] Young and Cheatham ions parameters for gromacs

Thanks in advance, Harut -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] nmr distance restraints

.e+00) functype[1044]=DISRES, label= 6, type=1, low= 3.0303e-01, up1= 3.0303e-01, up2= 4.3502e-01, fac= 1.e+00) etc... Any suggestions about what is wrong here would be appreciated Thanks, Eiso -- David van der Spoel, Ph.D., Professor of Biolog

Re: [gmx-users] OPLS parameters for O2

. Sci. U.S.A. 2008, 105, 1198−1203. that we have tested in the paper below and it has has quite accurate solubility in water. See Michiel van Lun, Jochen S. Hub, David van der Spoel and Inger Andersson: CO2 and O2 Distribution in Rubisco Suggests the Small Subunit Functions as a CO2 Reservoir J.

Re: [gmx-users] Implicit Solvent with User Defined Potentials

? Thank you for your help. Kind regards, Akash GB has been removed from GROMACS and if old versions do not have this option it seems you are out of luck. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-7

Re: [gmx-users] How to calculate tetrahedral order parameter in GROMACS

n and David van der Spoel: Order parameters and algorithmic approaches for detection and demarcation of interfaces in hydrate-fluid and ice-fluid systems J. Chem. Theor. Comput. 10 pp. 5606-5616 (2014) -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecula

Re: [gmx-users] MW particle type in TIP4Pew

ave a mass. Any suggestions will be helpful. Thanks in advance. Regards, Mandar Kulkarni -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.u

Re: [gmx-users] Energy Conservation at the Beginning of a Production Run

-1851390.153947 2.40 -1851390.238681 2.50 -1851390.144512 2.60 -1851390.255200 2.633000 -1851390.178012 From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of David van der Spoel Sent: Thursday, March 28, 2019 3:10:05 PM

Re: [gmx-users] Energy Conservation at the Beginning of a Production Run

? Please check options like ; Do not constrain the start configuration continuation = no Thank you! Luke -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.

Re: [gmx-users] All water molecules inside protein

all water molecules within let's say 0.3 nm distance from any atom belonging the protein. What is a simple and effective way to find only those water molecules which are within 0.3 nm distance from protein, please? Best wishes, Dawid Grabarek gmx trjorder -- David van der Spoel, Ph.D., Profe

Re: [gmx-users] gmx covar and gmx anaeig

Istanbul Medipol University Kavacik Mah., Ekinciler Cad. No:19 34810 Beykoz, Istanbul e-mail: osen...@medipol.edu.tr Phone:+90 (216) 681-5100 <%280216%29%20681%2051%2000> (5621) <http://ipont.medipol.edu.tr/> -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell

Re: [gmx-users] Gromacs 5.1.4 with GTX 780TI on Ubuntu 16.04; upgraded with GTX1080TI

Ti Result = PASS -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se -- Gromacs Users mailing list * Please search the archive at http://www

Re: [gmx-users] about 165 gromacs bug in the list

know of. If you have a reproducible case please upload to the redmine issue. The problem has been to get just such a case. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +4618471

Re: [gmx-users] Surface Energy calculation of polymeric materials

e may need application of polarizable models. Maria Luisa Maria Luisa Perrotta Ph.D Student, CNR-ITM via P.Bucci, 87036 Rende (Cs) Italy email: ml.perro...@itm.cnr.it -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box

Re: [gmx-users] Mean square displacement on Log-Log plot?

om/science/article/pii/S0005273616300219 Thanks! Kevin On Mon, Dec 10, 2018 at 3:34 PM David van der Spoel wrote: Hi, unusual request, but here goes. I am dealing with a referee to one of my papers who is asking for a mean square displacement plots: "a log-log plot of the MSD vs. time, fro

[gmx-users] Mean square displacement on Log-Log plot?

ually reached." Any clue what the referee is looking for? References? Cheers, -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se -- Gromacs User

Re: [gmx-users] [ implicit_genborn_params ] for Gromos54a7 FF

Den 2018-12-04 kl. 22:49, skrev Alex: Hi David, Thank you. On Tue, Dec 4, 2018 at 4:24 PM David van der Spoel wrote: Den 2018-12-04 kl. 21:58, skrev Alex: Dear all. I wonder where the [ implicit_genborn_params ] section should come in the below topol.top file for which the Gromos54a7 force

Re: [gmx-users] [ implicit_genborn_params ] for Gromos54a7 FF

- Thank you Regards, Alex -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se -- Gromacs Users mailing list * Please search the archive at http

Re: [gmx-users] g++ compiling with gromacs library

t 12:18 PM Alexander Tzanov < alexander.tza...@csi.cuny.edu> wrote: Use -I/path to your include directory in CFLAGS. On Nov 21, 2018 2:59 PM, David van der Spoel wrote: Den 2018-11-21 kl. 19:09, skrev Kit Sang Chu: Hi everyone, I have a Makefile from my colleague and I am trying to ma

Re: [gmx-users] g++ compiling with gromacs library

in advance. Simon -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se -- Gromacs Users mailing list * Please search the archive at http://www.groma

Re: [gmx-users] multiple electric fields

it in the code with some effort. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se -- Gromacs Users mailing list * Please search the ar

Re: [gmx-users] Calculation chi angle for tryptophan residue

: hzu...@gmail.com -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se -- Gromacs Users mailing list * Please search the archive at http://www.gromacs

Re: [gmx-users] multiple electric fields

z): E0_1 + E0_2*something-sinusoidal? For instance, can we have multiple 'electric-field-z' statements, each describing the desired portion? Thanks, Alex -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box

Re: [gmx-users] GMX Helix Segmentation fault

uggest any idea how should I get reed of this. Thanking you With Warm Regards Budheswar -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se --

Re: [gmx-users] simulation in acidic condition

g_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75

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