Re: [gmx-users] salt concentration

I think that's high school stuff. :) N -- number of ions. V = a^3 -- volume (a is cube side length) n -- concentration (1M = 6e+26 m-3, you have 0.002 M) N = a^3*n > 1 a > (1/n)^(1/3). On 11/14/2017 12:44 AM, Netaly Khazanov wrote: It makes sense. I am not sure that I follow how you

Re: [gmx-users] salt concentration

It makes sense. I am not sure that I follow how you calculated the critical box size depending on the the concentration. On Tue, Nov 14, 2017 at 9:12 AM, Alex wrote: > It makes no difference whether you use -np/-nn or -conc. Your box is > simply too small to result in a

Re: [gmx-users] salt concentration

It makes no difference whether you use -np/-nn or -conc. Your box is simply too small to result in a nonzero ion count with something like 0.002 M. The check is rather simple: a cubic box has to be larger than (1/n)^(1/3). For 0.002 M, that critical box size is 9.4 nm. You can of course force

Re: [gmx-users] salt concentration

Thanks for your prompt replay. I thougnt it would be more elegant way to do it using the commands. If not that is what I am going to do. Best, Netaly On Mon, Nov 13, 2017 at 2:37 PM, Hermann, Johannes < j.herm...@lrz.tu-muenchen.de> wrote: > Hi Netaly, > > one way would be to calculate the

Re: [gmx-users] mobile ligand with intermolecular interactions

On 11/13/17 3:00 AM, Ahmet Yildirim wrote: Sorry. The pymol and GROMACS give the same results for every three target dihedrals. The updated results are here: https://www.dropbox.com/s/7qgn7qa4rf2yc14/dih.pdf?dl=0 The results show that the average dihedrals are almost the same in both the

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

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 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,

Re: [gmx-users] Problem using gmx wham

At least upgrade to the latest release in the series (5.1.4) or better yet, the actual latest version (2016.4) to see if this is a bug that's been fixed. I seem to recall this same behavior reported before and subsequently solved, but haven't dug it up. -Justin On 11/13/17 7:11 AM,

[gmx-users] Protein almost detaching from the micellar core

Hi all, I am simulating a membrane protein embedded in a detegent micelle (didodecyl maltoside DDM micelle). I am using total 167 number of DDM monomers and 17 cholesterol hemisuccinate (CHS) molecules for mimicking experimental conditions under which it has been attempted to be crystallized.

Re: [gmx-users] Compilation error - Gromacs 2016.4

Dear Mark, Your guess is great :) Thanks for advising me to use version control. Best regards, *Lan Hoa* 2017-11-13 18:18 GMT-06:00 Mark Abraham : > Hi, > > That should never happen - which compiler was it? and are you sure this is > unmodified 2016.4? > > Mark > > On

Re: [gmx-users] Compilation error - Gromacs 2016.4

Hi, That should never happen - which compiler was it? and are you sure this is unmodified 2016.4? Mark On Mon, Nov 13, 2017 at 3:17 PM Hoa Trinh wrote: > Dear GMX users, > I encountered the following error when compiling Gromacs 2016.4: > > error: expected

[gmx-users] Compilation error - Gromacs 2016.4

Dear GMX users, I encountered the following error when compiling Gromacs 2016.4: error: expected primary-expression before ‘>’ token k_S = load(coeff); Does anyone face the same situation? What is the solution? Thanks in advance. Best regards, *Lan Hoa* -- Gromacs Users mailing

Re: [gmx-users] Ewald summation in 2 dimensions with correction

Hi, I am using gmx potential to measure the electric field. I've reported the values from field.xvg in my previous email. The field at the edges of the ionic liquid near the walls will oscillate because of the electric double layer but it is the bulk field I am concerned with. I read the

Re: [gmx-users] salt concentration

Hi Netaly, one way would be to calculate the number of Na, Cl, and Mg ions by hand, i.e. with the box size and the respective concentrations, and add the correct amount of ions in two steps, with the flags -np or -nn. E.g. in the first step you add Na and Cl and in the second you add Mg.

[gmx-users] salt concentration

Dear Gromacs User, Is it possible to simulate system with two salt concentrations , e.g. NaCl 0.1 mol/L and MgCl2 0.002 mol/liter? The commands that i am using you can see below: grompp_d -f ions.mdp -c ligand_MG_box_water.gro -p topol.top -o ions.tpr genion_d -s ions.tpr -o

Re: [gmx-users] Problem using gmx wham

Hey guys, Sorry if it seems that I'm bumping this thread, but I was wondering if anyone had any other suggestions before I let this thread die. Thanks. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se

[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 *

[gmx-users] Pİezoelectricity analyse

Hi, İ am newbie in Gromacs i processed pvdf(polymer) simulation in Gromacs for analyze piezoelectricity effect of pvdf in the different pressure and temperature.(using gmx dipole) Can i process different methods for analyze piezoelectric effect of pvdf. İ only know analyze dipole moments of

Re: [gmx-users] mobile ligand with intermolecular interactions

Sorry. The pymol and GROMACS give the same results for every three target dihedrals. The updated results are here: https://www.dropbox.com/s/7qgn7qa4rf2yc14/dih.pdf?dl=0 The results show that the average dihedrals are almost the same in both the state A and state B for both [dihedrals] or