[gmx-users] gmx trjconv does not produce exact .gro file (slightly different box length)

. Anyone knows why? (I should add that I have tried looking at different frames and different choices in -pbc flag, but still see the problem ) Best regards --- Faezeh Pousaneh Postdoc researcher Department

[gmx-users] structure

Hi, I have a mixture of two component system. I want to investigate the final structure, mainly the angles and orientations between different molecules and atom. Anyone has idea how to do that? thanks. Best regards -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] rdf at contact

I will be grateful if some one can reply my question, Best regards On Wed, May 30, 2018 at 4:45 PM, Faezeh Pousaneh wrote: > Hi, > > I have a system of similar molecules, I would like to obtain the rdf at > contact (meaning, at surface of one particle). > What I try is; I mak

[gmx-users] rdf at contact

Hi, I have a system of similar molecules, I would like to obtain the rdf at contact (meaning, at surface of one particle). What I try is; I make an index file containing only central atoms of all molecules, then I run: gmx rdf -f NPT.xtc -s NPT.tpr -n index.ndx -pbc -ref 1 -sel 0 -b

Re: [gmx-users] Gromacs Tutorial by Justin

different results from them. Why? Best regards On Wed, Mar 7, 2018 at 2:54 PM, Faezeh Pousaneh <fpoosa...@gmail.com> wrote: > Thank you. > > > Best regards > > > On Wed, Mar 7, 2018 at 1:38 PM, Justin Lemkul <jalem...@vt.edu> wrote: > >> >

[gmx-users] thermostat and barostat

Hi, I simulate a system which is very sensitive to chosen thermostat and barostat. I see information in Gromacs webpage (*http://www.gromacs.org/Documentation/Terminology/Thermostats *) that some thermostat are not good for systems

Re: [gmx-users] Gromacs Tutorial by Justin

Thank you. Best regards On Wed, Mar 7, 2018 at 1:38 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 3/7/18 6:24 AM, Faezeh Pousaneh wrote: > >> Dear Justin, >> >> I have 2 questions regarding your tutorial on Carbon Dioxide in this link: >>

[gmx-users] Gromacs Tutorial by Justin

Dear Justin, I have 2 questions regarding your tutorial on Carbon Dioxide in this link: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/vsites/index.html 1- I see that in your simple simulation you use no boundary conditions, pbc=no, should it be always so for this model?

[gmx-users] shear viscosity

Hi I want to obtain shear viscosity for ionic mixtures. I use the method Berk Hess gives in his paper, (J. Chem. Phy *116*, 209 (2002)). I would like to know if this is a better method, or the muller-plathe method (Phy. rev. E *59*, 5 (1999))? Best regards -- Gromacs Users mailing list *

Re: [gmx-users] rlist- group scheme

ards > > > > > > > > > > > > > > > > > > On Sun, Jan 21, 2018 at 12:57 AM, Mark Abraham < > > > > mark.j.abra...@gmail.com > > > > > > > > > > > > wrote: > > > > > > > >

Re: [gmx-users] rlist- group scheme

> mark.j.abra...@gmail.com > > > > > > > > wrote: > > > > > > > > > Hi, > > > > > > > > > > Yes, you said that before. But I asked what range it worked over, > ie > > > what > > > > > range o

Re: [gmx-users] rlist- group scheme

.j.abra...@gmail.com > > > > wrote: > > > > > Hi, > > > > > > Yes, you said that before. But I asked what range it worked over, ie > what > > > range of cutoff. > > > > > > Mark > > > > > > On Sat, Jan 20, 2018

Re: [gmx-users] rlist- group scheme

ist, not at rcut-off. how to deal with it now? Best regards On Sun, Jan 21, 2018 at 12:57 AM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > Hi, > > Yes, you said that before. But I asked what range it worked over, ie what > range of cutoff. > > Mark > > On Sat, Ja

Re: [gmx-users] rlist- group scheme

ham <mark.j.abra...@gmail.com> wrote: > Hi, > > There could be. But over what range does your table work correctly? What do > you get when you have a two particle system at various displacements? > > Mark > > On Fri, Jan 19, 2018, 23:59 Faezeh Pousaneh <fpoosa.

Re: [gmx-users] rlist- group scheme

utomating all this, but as you > know, there's not yet support for tabulated interactions. > > Mark > > On Fri, Jan 19, 2018, 14:25 Faezeh Pousaneh <fpoosa...@gmail.com> wrote: > > > Hi, > > > > I run a simple example using Table,6,12 (for LJ) with vdW type=

[gmx-users] rlist- group scheme

Hi, I run a simple example using Table,6,12 (for LJ) with vdW type= user. Then group scheme should be chosen. In results, I got different LJ energies when I set rlist=rcoulomb and rlist>rcoulomb (which is allowed in this scheme). I see in the manual that with group scheme that can be happen. But

Re: [gmx-users] rlist

then as (I > think) I've said before, you should consider alternative software (not that > I have any insight about what might work better). > > Mark > > On Mon, Jan 15, 2018 at 11:26 AM Faezeh Pousaneh <fpoosa...@gmail.com> > wrote: > > > Hi, > > > &g

[gmx-users] rlist

Hi, I have a user-potential for vdw and coulomb (PME-user). I use vdW and columnb cutoffs= 0.3 and 0.5 respectively. What should be the value of rlist? sorry, I could not find in manual. Best regards -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] rlist

Thanks a lot, Best regards On Sun, Jan 14, 2018 at 5:32 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 1/14/18 11:29 AM, Faezeh Pousaneh wrote: > >> Thank you Justin, now I understood. However, I do not have any target data >> for my system. What do yo

Re: [gmx-users] rlist

Thank you Justin, now I understood. However, I do not have any target data for my system. What do you suggest? the longer rcoulomb is safer, right? Best regards On Sun, Jan 14, 2018 at 4:47 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 1/14/18 10:42 AM, Faezeh

Re: [gmx-users] rlist

14, 2018 at 3:46 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 1/14/18 6:01 AM, Faezeh Pousaneh wrote: > >> Hi, >> >> I have a system of charged hard spheres (user-potential), where the vdW >> cut-off should be diameter of my molecule 0.3479. I

[gmx-users] rlist

Hi, I have a system of charged hard spheres (user-potential), where the vdW cut-off should be diameter of my molecule 0.3479. I wonder if I chose rlist and rcoulomb correctly? (see below please) integrator= md dt= 0.001 nsteps=

Re: [gmx-users] The sum of the two largest charge group radii (X) is larger than rlist

Thanks Justin. One component I mean system of only one type atom, each atom has two charged virtual sites. So I can not see from VMD any breaking. On Dec 17, 2017 8:10 PM, "Justin Lemkul" <jalem...@vt.edu> wrote: On 12/17/17 8:22 AM, Faezeh Pousaneh wrote: > Dear Justin,

Re: [gmx-users] The sum of the two largest charge group radii (X) is larger than rlist

Dear Justin, How can I check that ''input configuration is "broken" across PBC'' ? >From vmd it is hard to say, since I only have one component system. Best regards On Fri, Dec 15, 2017 at 2:05 PM, Faezeh Pousaneh <fpoosa...@gmail.com> wrote: > > The sum of the two l

Re: [gmx-users] The sum of the two largest charge group radii (X) is larger than rlist

; On 12/15/17 4:26 AM, Faezeh Pousaneh wrote: > >> Hi, >> >> I get this error only in NVT equlibration step, not in the NPT and >> production steps. Should I worry about it? >> >> In gromacs page it tell the error can come from 4 reasons, but how I can >>

[gmx-users] The sum of the two largest charge group radii (X) is larger than rlist

Hi, I get this error only in NVT equlibration step, not in the NPT and production steps. Should I worry about it? In gromacs page it tell the error can come from 4 reasons, but how I can recognize which can be mine?

Re: [gmx-users] virtual site connected to dummy massive site

<mark.j.abra...@gmail.com> wrote: > Hi, > > On Sun, Nov 26, 2017 at 6:35 PM Faezeh Pousaneh <fpoosa...@gmail.com> > wrote: > > > Hi Mark, sorry I am not convinced yet. I hope you did not misunderstand > my > > question, I have no charges in systems on any

Re: [gmx-users] virtual site connected to dummy massive site

the DOF change) then you > will not sample the same states. > > Mark > > On Fri, Nov 24, 2017 at 10:56 AM Faezeh Pousaneh <fpoosa...@gmail.com> > wrote: > > > Dear Mark, > > thanks, but degrees of freedom goes to kinetic energies, still LJ > energies > > must be

Re: [gmx-users] virtual site connected to dummy massive site

so they sample > difference spaces. The energies you observe reflect that difference. > > Mark > > On Mon, 20 Nov 2017 18:18 Faezeh Pousaneh <fpoosa...@gmail.com> wrote: > > > Hi, > > > > I have a system containing of a virtual site of carbon connected > >

[gmx-users] virtual site connected to dummy massive site

Hi, I have a system containing of a virtual site of carbon connected symmetrically to two dummy massive sites (no charge). like : M---C---M My problem is the results I get from simulation of this system is not equal with results of single Carbon system simulation with mass of 2M (at exactly

[gmx-users] c_6 and c_12 to zero

Hi, I have a simple system of non-charged diatomic molecule, (A-B). I expect total LJ interaction energy in such system when we put LJ parameters of atom B zero (c6 and c12=0) should be equal with total LJ energy of a system containing only atom A. Am I right? Best regards -- Gromacs Users

[gmx-users] virtual site, dummy massive site LJ interactions

Hi, I have 2 questions please. They seem evident, but I need to be sure to solve my simulation problem: 1- Does being a virtual site (charge, no mass) or a normal atom, effects on its LJ interaction energies with rest of system? 2- Does adding a dummy massive site (no charge, only mass) to

[gmx-users] virtual site, dummy massive site

I have 2 questions please. They seem evident, but I need to be sure to solve my simulation problem: 1- Does being a virtual site (charge, no mass) or a normal atom, effects on its LJ interaction energies with rest of system? 2- Does adding a dummy massive site (no charge, only mass) to atoms of

[gmx-users] (no subject)

Hi, I have a simple system of non-charged diatomic molecule, (A-B). I expect total LJ interaction energy in such system when we put LJ parameters of atom B zero (c6 and c12=0) should be equal with total LJ energy of a system containing only atom A. Am I right? Best regards -- Gromacs Users

Re: [gmx-users] force fileds gromos and oplsaa

Thanks a lot Justin! Best regards On Thu, Nov 16, 2017 at 2:31 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 11/16/17 8:28 AM, Faezeh Pousaneh wrote: > >> Hi >> >> sorry for silly question, but I did not find my answer by searching. >> >>

[gmx-users] force fileds gromos and oplsaa

Hi sorry for silly question, but I did not find my answer by searching. In gromos force fields, the file nonbonded.itp includes nonbonded parameters for two different atoms, e.g C O 1 2.300953E-03 2.222000E-06 while I do not see oplsaa provides parameters for nonbonded interactions of

Re: [gmx-users] GROMOS bond-stretching parameters

Thank you! Best regards On Tue, Nov 14, 2017 at 3:36 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 11/13/17 5:24 AM, Faezeh Pousaneh wrote: > >> Hi, >> Unfortunately I do not find in Gromos literature what is the third number >> in front of >>

[gmx-users] GROMOS bond-stretching parameters

Hi, Unfortunately I do not find in Gromos literature what is the third number in front of bond stretching parameters, e.g 1200 below: : ; ICB(H)[N]CB[N] B0[N] #define gb_50.1230 1.6600e+07 ; C - O1200 someone please tell me, Best regards -- Gromacs Users mailing list *

Re: [gmx-users] only interaction inside the molecule

umentation/How-tos/Tabulated_Potentials > > Best, > Yu > > -- > Du, Yu > PhD Student, > Shanghai Institute of Organic Chemistry > 345 Ling Ling Rd., Shanghai, China. > Zip: 200032, Tel: (86) 021 5492 5275 > > > -Original Messages- > > From: "

[gmx-users] only interaction inside the molecule

Hi, I would like an atom of my molecule only interact (LJ) with its own molecule, not the rest of system, how can I do that? thanks for reply, Best regards -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

Re: [gmx-users] dipole on an atom

virtual sites plus shell (drude) particle. which unfortunately there is little information in the manual. Best regards On Mon, Nov 6, 2017 at 5:16 PM, Faezeh Pousaneh <fpoosa...@gmail.com> wrote: > I think I have my answer to my initial question; how to give an atom a > dipole?

Re: [gmx-users] dipole on an atom

I think I have my answer to my initial question; how to give an atom a dipole? One can use virtual sites. Best regards On Mon, Nov 6, 2017 at 3:03 PM, Faezeh Pousaneh <fpoosa...@gmail.com> wrote: > David, > do you thin that Stockmayer potential can be implemented by user-specified

Re: [gmx-users] dipole on an atom

David, do you thin that Stockmayer potential can be implemented by user-specified potential? Best regards On Sun, Nov 5, 2017 at 4:18 PM, David van der Spoel <sp...@xray.bmc.uu.se> wrote: > On 05/11/17 16:07, Faezeh Pousaneh wrote: > >> Yes, exactly. But my atom is unch

Re: [gmx-users] non-neutral system

the literature for > >> further details. > >> > >> I don't know much about viscosity, so I'll leave that for someone else. > >> > >> Cheers, > >> J > >> > >> On Mon, Nov 6, 2017 at 11:50 AM, Faezeh Pousaneh <fpoosa...@gma

Re: [gmx-users] non-neutral system

ystem's charge. ​It's a >> limitation of the Ewald summation. Take a look at the literature for >> further details. >> >> I don't know much about viscosity, so I'll leave that for someone else. >> >> Cheers, >> J >> >> On Mon, Nov 6, 2017 at 11:50

[gmx-users] non-neutral system

Hi, I have a system containing similar charged atoms. So the total charge is not zero. Simulation results with cut-off coulomb seems reasonable, but using PME they are wrong (total columb potential is negative value which must be positive). Any idea why? If I use counter-ions to neutralize

Re: [gmx-users] dipole on an atom

Yes, exactly. But my atom is uncharged sphere, I'll bring two similar size and similar mass (+ -) ions inside the sphere. So rotation will not happen then for atom. On Nov 5, 2017 16:00, "David van der Spoel" <sp...@xray.bmc.uu.se> wrote: On 05/11/17 15:54, Faezeh Pousaneh wrot

Re: [gmx-users] dipole on an atom

;sp...@xray.bmc.uu.se> wrote: > On 04/11/17 19:19, Faezeh Pousaneh wrote: > >> Hi, >> >> I have an uncharged atom, and I would like to give it a dipole. Any >> suggestion? >> > impossible in gromacs. > >> >> Best regards >> >> > &

[gmx-users] dipole on an atom

Hi, I have an uncharged atom, and I would like to give it a dipole. Any suggestion? Best regards -- 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

[gmx-users] viscosity from periodic perturbation method

Hi, My simulation results for viscosity calculation strongly depends on the chosen amplitudes of the acceleration profiles in the .mdp file (!?). How to estimate acceleration amplitude values? appreciate if someone can answer, Best regards -- Gromacs Users mailing list * Please search the

Re: [gmx-users] User-specified potential functions

Solved!! the constant can be added to the table, to g(r) or h(r). Best regards On Tue, Oct 24, 2017 at 7:05 PM, Faezeh Pousaneh <fpoosa...@gmail.com> wrote: > Hi, > > I created a table for my own potential which has a 'constant' value. I > added it to the g(r) or h(r) func

[gmx-users] User-specified potential functions

Hi, I created a table for my own potential which has a 'constant' value. I added it to the g(r) or h(r) functions in the table, but it gives incorrect results. I also can not shift the potential after simulation, since the x>cut-off will be also shifted. Any suggestion? Best regards -- Gromacs

[gmx-users] non-zero total charge

Hi, I am simulating one component system (tabulated potential), and they have similar charge. So the total charge of the system is non-zero. The program properly works. Should I still worry? Thanks for answer Best regards -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Fwd: shift the LJ potential

rious > conditions. Details of what and how do vary with the force field, are are > documented in its literature, of course. > > Mark > > On Wed, Oct 11, 2017 at 3:43 PM Faezeh Pousaneh <fpoosa...@gmail.com> > wrote: > >> Apart from my own simulation, I do no understand

Re: [gmx-users] Fwd: shift the LJ potential

2017 at 5:06 AM, Faezeh Pousaneh <fpoosa...@gmail.com> > wrote: > >> Thank you Wes and Mark, >> >> Wes, that is what I am trying to do. However, still have problem. >> I do not know how to derive sigma, epsilon (or C6 and C12) for my >> particle? >> How

Re: [gmx-users] Fwd: shift the LJ potential

:55 PM, Wes Barnett <w.barn...@columbia.edu> wrote: > On Tue, Oct 10, 2017 at 5:42 AM, Faezeh Pousaneh <fpoosa...@gmail.com> > wrote: > > > Hi Mark > > > > I have a given function for pseudo hard-sphere potential, which has > > different powers than LJ

[gmx-users] Fwd: shift the LJ potential

pling - only the forces do. How does that affect what you're thinking of? Mark On Mon, Oct 9, 2017 at 3:14 PM Faezeh Pousaneh <fpoosa...@gmail.com> wrote: > Hi, > > I would like to shift the LJ interaction between my particle by a constant, > (to remove attraction), how can I change

Re: [gmx-users] shift the LJ potential

pling - only the forces do. How does that affect what you're thinking of? Mark On Mon, Oct 9, 2017 at 3:14 PM Faezeh Pousaneh <fpoosa...@gmail.com> wrote: > Hi, > > I would like to shift the LJ interaction between my particle by a constant, > (to remove attraction), how can I change

[gmx-users] shift the LJ potential

Hi, I would like to shift the LJ interaction between my particle by a constant, (to remove attraction), how can I change the function? Best regards -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! *

[gmx-users] not specific molecule or atom

Hi I am trying to simulate 'sphere particles' with a diameters with specific interactions among them. How can I have my own particles not a defined molecules or atoms in the force fields. thanks for answer, Best regards -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Cutting simulatio box

ou ask for a 'phase', which usually > involves many particles, but it appears that it's that same single > molecule? That changes matters quite a bit, as whatever you're going to > look at is going to be pretty noise. > > What is your objective? > > Cheers, > > Tsjer

Re: [gmx-users] Cutting simulatio box

ew groups as energy_grps. That would give you the > within and between group energies. > > Hope it helps, > > Tsjerk > > On Jul 18, 2016 12:49 PM, "Faezeh Pousaneh" <fpoosa...@gmail.com> wrote: > > Hi, > > I have a Phase-separation in my simulation result. I

[gmx-users] Cutting simulatio box

Hi, I have a Phase-separation in my simulation result. I need to find energy between molecules at each phase. Can I cut the box into small boxes, each having one phase, and then by extension the run (with similar setting as original) obtain the energies at each phase? Thank you! Best regards --

Re: [gmx-users] g_select, only 'one' water within z>=10 and z<=10.1

ut from the first selection the molecule or atom indices > that suit you. I assume that can be done in one call to gmx select, but the > details are an exercise for the reader :-P > > Mark > > On Fri, 15 Jul 2016 15:52 Faezeh Pousaneh <fpoosa...@gmail.com> wrote: > > > I u

Re: [gmx-users] g_select, only 'one' water within z>=10 and z<=10.1

I undrestand my command is not correct for having one water. So it is my question how to change the command to have a single molecule? Best regards On Fri, Jul 15, 2016 at 3:35 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 7/15/16 9:28 AM, Faezeh Pousaneh wrote: > &

[gmx-users] g_select, only 'one' water within z>=10 and z<=10.1

Hi, I want to select only a 'single' water molecule at specific part of my simulation box. So I try: g_select-selrpos whole_mol_com and select resname SOL and z >= 10 and z <= 10.1 But depending on time frame I get more than one molecules or sometimes no molecules. How can I fix it?

Re: [gmx-users] Energy between desired selected molecules

is how properly re-name the energy groups in .mdp file according to the index file which has so many frames? Thank you for help. Best regards On Fri, Jul 1, 2016 at 4:20 PM, Faezeh Pousaneh <fpoosa...@gmail.com> wrote: > Thank you again :) > > > Best regards > > >

Re: [gmx-users] Energy between desired selected molecules

Thank you again :) Best regards On Fri, Jul 1, 2016 at 4:17 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 7/1/16 10:05 AM, Faezeh Pousaneh wrote: > >> Thank you Justin and Mark for the help. I could obtain. >> >> More details for someone with simila

Re: [gmx-users] Energy between desired selected molecules

, 2016 at 2:38 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 7/1/16 8:36 AM, Faezeh Pousaneh wrote: > >> Thank you both, I am close to solve it. The remaining problem is when I >> mdrun -rerun, it tells the number of atoms in old trajectory is not the >> sam

Re: [gmx-users] Energy between desired selected molecules

l 1, 2016 at 2:19 PM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > Hi, > > Yes as Justin says, a group is a few molecules that you selected :-) > > Mark > > On Fri, 1 Jul 2016 14:00 Justin Lemkul <jalem...@vt.edu> wrote: > > > > > > > On 7/1/1

Re: [gmx-users] Energy between desired selected molecules

trajectory, however. > > Mark > > On Fri, Jul 1, 2016 at 9:41 AM Faezeh Pousaneh <fpoosa...@gmail.com> > wrote: > > > Hi > > > > Does someone know how to obtain energy between specific molecules in the > > system? > > > > What I did and seems n

[gmx-users] Energy between desired selected molecules

Hi Does someone know how to obtain energy between specific molecules in the system? What I did and seems not be correct is: 1- I obtained the molecules I wanted to look at: g_select_mpi -f 600gro.gro -s production.tpr -on 2- Then I produced a .tpr file for the chosen selection,index.ndx,

Re: [gmx-users] Partial density versus time

, Faezeh Pousaneh <fpoosa...@gmail.com> wrote: > Hi Tsjerk > > I attach a picture what I explicitly want. Your approach shows of course > the appearance of the phase separation, but I necessarily need the time > evolution of density of one component to see 'how' it reac

Re: [gmx-users] Partial density versus time

Dear Tsjerk, no that does not give what I want. Best regards On Thu, Apr 7, 2016 at 6:41 PM, Faezeh Pousaneh <fpoosa...@gmail.com> wrote: > Hi Negar, > > I tried your solution, but still it does not give the density (of each > component) versus time. It gives densi

Re: [gmx-users] Partial density versus time

Tsjerk > On Apr 6, 2016 17:10, "Faezeh Pousaneh" <fpoosa...@gmail.com> wrote: > > > Hi Tsjerk, > > > > Thanks, but my question it is not that simple. > > I am dealing with phase separation of a two-component system. At the end > of > > simul

Re: [gmx-users] Partial density versus time

only once! > > Let me know if you need more explanation, > Best, > Negar > > On Wed, Apr 6, 2016 at 4:59 PM Faezeh Pousaneh <fpoosa...@gmail.com> > wrote: > >> Thanks Negar. >> >> More detail; my system phase-separate after equilibrium, such that eac

Re: [gmx-users] Partial density versus time

he results to have a density > profile over time. > > Hope it helps, > > Tsjerk > > On Wed, Apr 6, 2016 at 4:29 PM, Faezeh Pousaneh <fpoosa...@gmail.com> > wrote: > > > Hi, > > > > Is it possible to obtain partial density versus time in Groma

Re: [gmx-users] Partial density versus time

If this is what you mean, I'll be happy to help with more information. >> >> Best, >> Negar >> >> >> On Wed, Apr 6, 2016 at 4:30 PM Faezeh Pousaneh <fpoosa...@gmail.com> >> wrote: >> >>> Hi, >>> >>> Is it possible to obtain p

[gmx-users] Partial density versus time

Hi, Is it possible to obtain partial density versus time in Gromacs? Precisely, I have a system of two components which separate by time. I need the evolution of density of each phase by time? thanks. Best regards -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Center of mass removal for a trajectory which is already created

, I used -fit obtain in trjconv to remove transnational movement of component 2: trjconv_mpi -fit translation -s production.tpr -f traj.xtc -o OUTPUT.xtc chose component 2 and 2, Then, I collect densities from produced OUTPUT.xtc. Best regards On Fri, Nov 13, 2015 at 1:38 PM, Faezeh Pousaneh

[gmx-users] Center of mass removal for a trajectory which is already created

Hi, Please some one help me how to remove center of mass motion in a trajectory which is already created without this setting? is that possible? thanks in advance, Best regards -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Center of mass removal for a trajectory which is already created

and run it with COM removal to collect density? Best regards On Fri, Nov 13, 2015 at 1:30 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 11/13/15 4:06 AM, Faezeh Pousaneh wrote: > >> Hi, >> >> Please some one help me how to remove center of mass motion in

Re: [gmx-users] cut-off

Thank you Justin, Best regards On Fri, Jun 19, 2015 at 2:40 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/18/15 7:47 AM, Faezeh Pousaneh wrote: Thanks Justin. yes, you are right, my simulation is very sensitive to cut-off. I did not understand what do you meant by '' is the balance

Re: [gmx-users] cut-off

a force field, could you tell me a proper force field for Benzene all-atom model? Best regards On Thu, Jun 18, 2015 at 1:37 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/18/15 7:25 AM, Faezeh Pousaneh wrote: thanks David. but I am wondering for example if a chosen short cut-off produces

Re: [gmx-users] cut-off

, Faezeh Pousaneh wrote: Hi, Does the choice of cut-off length depends on the chosen force filed? or it can be chosen such that the simulation produces the experimental values? Cutoff should be used consistently, each force field has their setting, however that does not mean these settings

Re: [gmx-users] Different Cv and Cp

distributions are being correctly generated: See the code and paper describing it linked here: https://github.com/shirtsgroup/checkensemble On Tue, Jun 9, 2015 at 11:23 AM, Faezeh Pousaneh fpoosa...@gmail.com wrote: Dear Michael, Can I ask a question concerning your previous email, I followed

[gmx-users] cut-off

Hi, Does the choice of cut-off length depends on the chosen force filed? or it can be chosen such that the simulation produces the experimental values? In my case, I simulation Benzene with Gromos54A7 and I choose 1.2 nm for both LJ and coul interactions, is that fine? thanks Best regards --

[gmx-users] compressibility

Hi, I simulate a molecule in NPT ensemble, which I can not find any experimental data about it's compressibility, what should I put in .mdp file for it's compressibility in pressure coupling? Best regards -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] compressibility

at 3:12 AM, Faezeh Pousaneh fpoosa...@gmail.com wrote: Hi, I simulate a molecule in NPT ensemble, which I can not find any experimental data about it's compressibility, what should I put in .mdp file for it's compressibility in pressure coupling? Best regards -- Gromacs Users

Re: [gmx-users] Different Cv and Cp

it to 0.2 I get a bigger C_v. best Andre On Wed, Jun 10, 2015 at 9:54 AM, Faezeh Pousaneh fpoosa...@gmail.com wrote: Dear Michael, Could you please comment on my last question, thanks a lot. I have noticed that when I run both NVT and NPT simulations from a same .gro file (obtained

Re: [gmx-users] Different Cv and Cp

Shirts mrshi...@gmail.com wrote: The variance formula is derived from the derivative formula + the assumption the distribution in Boltzmann, so they must agree if the distribution is Boltzmann. On Tue, Jun 9, 2015 at 11:43 AM, Faezeh Pousaneh fpoosa...@gmail.com wrote: Thank you so much

Re: [gmx-users] Different Cv and Cp

and estimate the derivatives. On Tue, May 26, 2015 at 5:12 AM, Faezeh Pousaneh fpoosa...@gmail.com wrote: Dear Michael, I still would like to know what was your method you mentioned on last paragraph, just for learning: ''Also, to be sure, you should double check by calculating both heat

Re: [gmx-users] Different Cv and Cp

The latter way, I meant in NPT and NVT simulation respectively. I noted that Gromacs produces Cv and Cp from the latter case. Best regards On Tue, Jun 9, 2015 at 5:23 PM, Faezeh Pousaneh fpoosa...@gmail.com wrote: Dear Michael, Can I ask a question concerning your previous email, I

Re: [gmx-users] Different Cv and Cp

, Faezeh Pousaneh fpoosa...@gmail.com wrote: Dear Michael, Can I ask a question concerning your previous email, I followed Cv = (dU/dT)_V Cp = (dH/dT)_P for my lutidine molecule, and I get same values for Cv and Cp. But when I test with kB T^2 c_P = Var (Enthalpy) kB T^2

[gmx-users] g_covar

Hi, I need help please. I am calculating entropy of a single water in water solution. So I did a 10 ns NPT. Then I run g_covar -f NPT.xtc -s NPT.tpr -o -l -av -v and g_anaeig_d -v eigenvec.trr -entropy -eig eigenval.xvg I have two questions. 1- In the g_covar it asks to select group,

[gmx-users] energy between different groups

Hi, I simulate liquid water 1397 molecules with specifying two groups with index file; 1 molecule and rest of the molecules 1396. When I obtain average LJ energy per molecule for whole system (with -nmol), I get 16 kJ/mol, but when I obtain it from interaction between groups,

[gmx-users] entropy of water

Hi, I need help please. I am calculating entropy of a single water in water solution. So I did a 10 ns with output NPT. Then I run g_covar -f NPT.xtc -s NPT.tpr -o -l -av -v and g_anaeig_d -v eigenvec.trr -entropy -eig eigenval.xvg I have two questions. 1- In the g_covar it asks to

[gmx-users] number of Nodes after extension

Hi, A question please, Can I change the number of nodes for the extension of the first run (let us say first run was with 10 nodes and now I want to increase it to 20 in the extension)? does that influence on the analysis of the runs? thanks. Best regards -- Gromacs Users mailing list * Please

Re: [gmx-users] number of Nodes after extension

Thanks Mark! Best regards On Fri, May 29, 2015 at 10:19 AM, Mark Abraham mark.j.abra...@gmail.com wrote: Yes you can do that. No, it doesn't matter. Mark On Fri, May 29, 2015 at 10:16 AM Faezeh Pousaneh fpoosa...@gmail.com wrote: Hi, A question please, Can I change the number

[gmx-users] Different Cv and Cp

Hi, I do not know why I obtain two difference cp and cv from NVT and NPT simulations. What I do is, I take 1000 lutidne molecules, and I do firstly an energy minimization with steep integrator, then NPT simulation at T=300 and P=1 atm for 10ns, (I obtain Cp= 230), then I run NVT for 10 ns with

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