Re: [gmx-users] question about torsional potential fitting

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Re: [gmx-users] Naughty Vacuum Bubble in our Vesicle!

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Re: [gmx-users] Naughty Vacuum Bubble in our Vesicle

to gmx-users-requ...@gromacs.org. -- _ Prof. Dr. André Farias de Moura Department of Chemistry Federal University of São Carlos São Carlos - Brazil phone: +55-16-3351-8090 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Naughty Vacuum Bubble in our Vesicle

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Re: [gmx-users] Pressure coupling and liquid crystals

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Re: [gmx-users] Silica monolayer with Martini force field

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Re: [gmx-users] Silica monolayer with Martini force field

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Re: [gmx-users] Silica monolayer with Martini force field

%, and water freezing appears in all cases. Any suggestion to avoid freezing in these simulations? thank you again for your help, Ramon Reigada University of Barcelona reig...@ub.edu El 29/10/2014, a las 15:05, André Farias de Moura escribió: Dear Ramon, we did something like

Re: [gmx-users] Question about water freezing when in contact to a solid surface (ramon)

. André Farias de Moura Department of Chemistry Federal University of São Carlos São Carlos - Brazil phone: +55-16-3351-8090 -- 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

Re: [gmx-users] how to remove water molecule inside micelle?

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Re: [gmx-users] RDF plot with large g(r) values

:34 AM, Kester Wong kester2...@ibs.re.kr wrote: Hi Andre, Thank you for your input. *보낸사람* : André Farias de Moura mo...@ufscar.br *받는사람* : Discussion list for GROMACS us gmx-us...@gromacs.org *받은날짜* : 2015년 1월 8일(목) 22:05:39 *제목* : Re: [gmx-users] RDF plot with large g(r) values RDF

Re: [gmx-users] RDF plot with large g(r) values

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Re: [gmx-users] Tetrahydrofuran OPLS-AA forcefield

Tritschel -- _ Prof. Dr. André Farias de Moura Department of Chemistry Federal University of São Carlos São Carlos - Brazil phone: +55-16-3351-8090 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting

Re: [gmx-users] Error

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Re: [gmx-users] Different Cv and Cp

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Re: [gmx-users] Coul-SR: positive value for interating group

/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- _ Prof. Dr. André Farias de Moura Department of Chemistry Federal University of São Carlos São Carlos - Brazil phone: +55-16-3351-8090 -- Gromacs Users mailing list * Please search the archive at http

Re: [gmx-users] Coul-SR: positive value for interating group

are additive, but this is not the same as decomposable! Mark On Wed, May 27, 2015 at 2:52 PM André Farias de Moura mo...@ufscar.br wrote: Raja, just guessing, based on the few informations you posted: if the local dipole moments of these groups are parallel to each other, interaction

Re: [gmx-users] Simulation of Ethanol

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Re: [gmx-users] g_rdf problem

, for example)? 2015-07-27 23:06 GMT+08:00 André Farias de Moura mo...@ufscar.br: RDF may behave just like that (slowly growing from 0 to 1 without peaks), meaning that you have a pair of sites without significant structure besides the excluded volume in the region where RDF 1. for instance

Re: [gmx-users] how to calculate ESP at certain position

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Re: [gmx-users] Eccentricity of Reverse Micelle

/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- _ Prof. Dr. André Farias de Moura Department of Chemistry Federal University of São Carlos São Carlos - Brazil phone: +55-16-3351-8090 -- Gromacs Users mailing list * Please search the archive at http

Re: [gmx-users] PBC in a closed box.

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Re: [gmx-users] how to calculate ESP at certain position

knowledge GROMACS does not have such a tool. So I suppose they write their own code. Here is the link of the paper: http://pubs.acs.org/doi/abs/10.1021/jp803661f 2015-08-04 21:30 GMT+08:00 André Farias de Moura mo...@ufscar.br: Dear Zhenyu, I would be careful with the choice of words: you

Re: [gmx-users] g_rdf problem

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Re: [gmx-users] RDF

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Re: [gmx-users] How to generate a model beta sheet

isit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- _ Prof. Dr. André Farias de Moura Department of Chemistry Federal University of São Carlos São Carlos - Brazil phone: +55-16-3351-8090 -- Grom

Re: [gmx-users] Electric double layer, how to add charge

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Re: [gmx-users] Free Energy of Liquid Water

ists > > * 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. > -- _ Prof. Dr. André Farias de Moura Department of Chemistry Federal University of São Carlos São C

Re: [gmx-users] Electric double layer, how to add charge

lem with the potential? > > Thanks again. > > Best regards > > Andreas > > > On Wed, Sep 16, 2015 at 23:33, André Farias de Moura wrote: > > you should edit your topology file (either top or itp) to include explicit >> charges to each atom. >> >>

Re: [gmx-users] addition of hydronium ion in simulation box

attached to a neighboring H2O molecule, which now has 3 identical H atoms, and then looses one of them to another neighboring H2O molecule and so on. I'm still testing it, but DFTB should do the trick as well. On Mon, Sep 21, 2015 at 11:36 PM, André Farias de Moura <mo...@ufscar.br>

Re: [gmx-users] addition of hydronium ion in simulation box

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Re: [gmx-users] Fw: thermodynamic integration

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Re: [gmx-users] topology of ligand contains boron

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Re: [gmx-users] Segmentation fault after merging two equilibrated molecules!

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Re: [gmx-users] Surface tension coupling with Parrinello-Rahman algorithm

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Re: [gmx-users] How many times should I do Umbrella Sampling

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Re: [gmx-users] liquid-solid/liquid-air interface simulations

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Re: [gmx-users] Optimum slice size (-sl)

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Re: [gmx-users] Fw: question

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Re: [gmx-users] Fw: question:Justin toturial

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Re: [gmx-users] Atom X in residue YYY was not found in rtp fil

to gmx-users-requ...@gromacs.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/Support/Mailing_Lists > > * For (un)s

Re: [gmx-users] NPT equilibration with small cell

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Re: [gmx-users] lipids in force field

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Re: [gmx-users] md of only water - obtaining different pressure in the x , y and z directions

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Re: [gmx-users] IR Spectra

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Re: [gmx-users] IR Spectra

x > > On Wed, Mar 2, 2016 at 4:32 PM, André Farias de Moura <mo...@ufscar.br> > wrote: > > > in a nutshell: you need to compute the velocity autocorrelation function > > and then its Fourier transform. > > > > you should mind about proper sampling of velocitie

Re: [gmx-users] Any way to not compute certain interactions?

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Re: [gmx-users] Parameterization of OPLS-AA force field for MoS2 simulation in GROMACS.

These two sets of units are > incommensurate, yes? > > > > On Wed, May 18, 2016 at 4:29 PM, André Farias de Moura <mo...@ufscar.br> > wrote: > > > Hi Barret, > > > > It looks like you just have to make the proper conversion of units (eV to > >

Re: [gmx-users] Parameterization of OPLS-AA force field for MoS2 simulation in GROMACS.

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Re: [gmx-users] Surface tension

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Re: [gmx-users] gmx potential and water

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Re: [gmx-users] Supercomputing facility

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Re: [gmx-users] binding free energy

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Re: [gmx-users] Negative pressure in an interface NVT simulation

> > > > > > I have tried to explain as much as possible to get the help, but if I am > > missing some information, please let me know and I will provide that. > > > > > > Thanks a lot. I look forward for some help. > > > -- > Gromacs Users mailing li

Re: [gmx-users] parameters for PbSe (quantum dot)

p://www.scopus.com/authid/detail.url?authorId=54886431500 > > http://www.ncbi.nlm.nih.gov/pubmed/?term=sako+mirzaie > https://www.researchgate.net/profile/Sako_Mirzaie/publications/ > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ &g

Re: [gmx-users] MD for inorganic compound

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Re: [gmx-users] Zinc Oxide Simulation

ribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. -- _ Prof. Dr. André Farias de Moura Department of Chemistry Federal University of São Carlos São Carlos - Brazil phone: +55-16-3351

Re: [gmx-users] non zero free energy values in mass transformation

something > like this or i have blundered somewhere? > > Will be happy to share input files if it helps. > > Thanks and Regards > > -- > Deepak U. Bapat > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mai

Re: [gmx-users] umbrella sampling

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Re: [gmx-users] Calculation of nematic order parameter using gromacs

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Re: [gmx-users] Difference in properties when method of adding urea molecules is changed in a simulation box

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Re: [gmx-users] Calculation of nematic order parameter using gromacs

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Re: [gmx-users] Can we calculate Potential of mean force from normal MD simulations

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Re: [gmx-users] Problem with center-of-mass RDF and subsequent coordination number calculation

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Re: [gmx-users] Ion pair

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Re: [gmx-users] Simulation in NPgT ensemble

sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. -- _ Prof. Dr. André Farias de Moura Department of Chemistry Federal University of São Carlos São Carlos - Brazil phone: +55-16-3351-8090 -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Surface tension for water

;> pcoupltyp? Am I right with semiisotropic options? > >>> > >>> > >>> Respectfully, > >>> Iman Ahmadabadi > >>> > >> > >> > >> > >> -- > >> Iman Ahmadabadi > >> > >> Sharif

Re: [gmx-users] SDS initial setup

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Re: [gmx-users] generating Topology file of Metal Oxide

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Re: [gmx-users] Radius of gyration and moment of inertia (Dallas Warren)

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Re: [gmx-users] Surfactant from experiments to MD simulation

st.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- _ Prof. Dr. André Farias de Moura Department of Chemistry Federal University of São Carlos São Carlos - Brazil phone: +55-16-3351-8090 -- Gromacs Users mailing list * Please sear

Re: [gmx-users] dos command for extracting vibrational spectra for a particular bond

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Re: [gmx-users] solvent evaporation modeling

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Re: [gmx-users] Vibrational spectra of amide I using gromacs

Carlos - Brazil > > phone: +55-16-3351-8090 > > > > > > -- > > > > > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >

Re: [gmx-users] Vibrational spectra of amide I using gromacs

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Re: [gmx-users] Simulate only one unit of the virus capsid while fixing its surrounding units

Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > == > > -- &g

Re: [gmx-users] Simulate only one unit of the virus capsid while fixing its surrounding units

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Re: [gmx-users] Simulate only one unit of the virus capsid while fixing its surrounding units

sition_Restraints > > > Thank you! > > > Yours sincerely > Cheng > -- > 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.groma

Re: [gmx-users] Fwd: Reproducibility of a PMF plot

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