Re: [gmx-users] Re: Trying to replicate Aqvist's results (solvation free energy).

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Re: [gmx-users] Trying to replicate Aqvist's results (solvation free energy).

://www.gromacs.org/Support/Mailing_Lists -- _ Prof. Dr. André Farias de Moura Department of Chemistry Federal University of São Carlos São Carlos - Brazil phone: +55-16-3351-8090 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please

Re: [gmx-users] Re: SMD - reproducibility

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Re: [gmx-users] surface tension

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Re: [gmx-users] Bonds - force constant for given Beads

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

, 2012 at 1:21 AM, Justin Lemkul jalem...@vt.edu wrote: On 11/19/12 10:04 PM, André Farias de Moura wrote: from the statistical thermodynamics standpoint, rdf must be the same for both choices of reference group, i.e.,solute-solvent and solvent-solute must yield exactly the same rdf, the only

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

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

/Mailing_Lists -- _ Prof. Dr. André Farias de Moura Department of Chemistry Federal University of São Carlos São Carlos - Brazil phone: +55-16-3351-8090 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http

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

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Re: [gmx-users] Autocorrelation of dipole moment

Farias de Moura mo...@ufscar.br sure, the ACF for a vector gives you the average cosine between that vector at time t=0 and the same vector at a later time lag, thus negative values may be seen as an inversion of the direction to which the vector points out (-1 would be the value

Re: [gmx-users] Autocorrelation of dipole moment

sure, the ACF for a vector gives you the average cosine between that vector at time t=0 and the same vector at a later time lag, thus negative values may be seen as an inversion of the direction to which the vector points out (-1 would be the value for a vector lying 180 degrees away from the

Re: [gmx-users] Re: micelles and trjconv -pbc cluster

Dear Tsjerk and Ran, I would like to try your modified versions of g_clustsize and trjconv as well since I am facing similar issues on the analyses of micellar systems. with kind regards, Andre On Thu, Apr 14, 2011 at 5:29 PM, jim jack blhaw...@yahoo.com wrote: Dear Ran Friedman and Tsjerk

Re: [gmx-users] compressing a box of water droplets into a homogeneous solution of liquid water

Hi Chris, recently one of my students made a mistake during the model system assembling, setting the initial volume to a value three times larger than expected by the density. after 1 microsecond (coarse grained MD, of course) there were droplets and vacuum between them, and the volume did not

[gmx-users] Re: surface tension

gen_seed    =  173529 constraints         = all-bonds constraint-algorithm = lincs == 2011/3/15 André Farias de Moura mo...@ufscar.br Dear Elisabeth, PBC are still there when you increase the box length in one direction, but that increase

[gmx-users] Re: surface tension

direction is reasonable? (If I have a 2 nm box). Also Can you please introduce some text book? Thank you, Best regards, 2011/3/15 André Farias de Moura mo...@ufscar.br Dear Elisabeth, actually, it is the other way around, you need increase the box length in one direction, thus keeping periodic

[gmx-users] Re: surface tension

Dear Elisabeth, actually, it is the other way around, you need increase the box length in one direction, thus keeping periodic boundary conditions in the other two directions while a (infinitely periodic) surface is created. and notice that using genconf with -nbox 3 3 1 will increase your system

Re: [gmx-users] surface tension in gmx

if you are interested in the surface tension of a pure liquid, which I assume is true from your message, then you need to create at least one surface, since periodic boundary conditions make the model system infinite, i.e., without a surface whatsoever. the easiest way to make that happen is to

Re: [gmx-users] surface tension in gmx

regarding your first question, the definition of gamma is not correct, you are getting energy/length⁴ instead of energy/area (multiply by Lz instead of dividing by it) 2011/3/9 Pedro Alexandre de Araújo Gomes Lapido Loureiro palap...@gmail.com: Hi, 1- g_energy is giving #Surf*SurfTen by

Re: [gmx-users] H-bond autocorrelation doubts

the manual does not enclose all the necessary knowledge for any kind of MD simulation or analyses, so you have to read some papers and textbooks as well. as I've already pointed out, g_hbond reads the whole set of frames, but the results are meaningful (in the sense of having a homogeneous

Re: [gmx-users] H-bond autocorrelation doubts

: Thanks for your suggestions. Can you please give some explanation for my second doubt... 2011/2/28 André Farias de Moura mo...@ufscar.br the manual does not enclose all the necessary knowledge for any kind of MD simulation or analyses, so you have to read some papers and textbooks as well.as

Re: [gmx-users] g_dipole

the program actually reads all frames, but it computes the correlation up to half of the total length of the data (it is a homoscedasticity issue, you should read some textbook on time series analysis before you increase the output length using -acflen) best André On Thu, Feb 24, 2011 at 5:04

Re: [gmx-users] Reg: Surface tension of water

did you increase the size of the box in one direction in order to create a water/vacuum interface on each side of the water slab? best, Andre On Tue, Dec 7, 2010 at 8:21 AM, vinothkumar mohanakrishnan kmvin...@gmail.com wrote: Hi all I want to calculate the surface tension of water using SPC

Re: [gmx-users] Reg: Surface tension of water

? Regards Vinoth 2010/12/7 André Farias de Moura mo...@ufscar.br did you increase the size of the box in one direction in order to create a water/vacuum interface on each side of the water slab? best, Andre On Tue, Dec 7, 2010 at 8:21 AM, vinothkumar mohanakrishnan kmvin...@gmail.com wrote

Re: [gmx-users] NAMD simulation in Gromacs

I have never tried it myself, but Wordom should be able to convert between dcd and xtc file formats, take a look at http://www.biochem-caflisch.unizh.ch/wordom/Home I hope it helps. best regards Andre On Thu, Sep 30, 2010 at 8:55 AM, Mark Abraham mark.abra...@anu.edu.auwrote: -

Re: [gmx-users] Mix two solvents

dear Rob, you can manually edit one of the gro file to increase the length in one direction by an arbitrary amount, then use genbox: genbox -cp edited file -cs the other gro file (I just did that with water and methanol from the gromacs tutorials, works just fine) maybe set -vdwd to an

Re: [gmx-users] Re: Forming a micelles

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Re: [gmx-users] OPLS atom types for THF simulations

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Re: [gmx-users] Some Issues on Substrates/PBC

-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 to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php * Prof. Dr. André Farias