[gmx-users] initial velocities

Dear all, I want to apply an initial velocity to my system. Is there a possible way rather than gen_vel in which I can chose my own wanted velocities? And if so, how can I introduce the vx,vy and vz for the atoms? thank you -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] initial velocities

Thank you very much Tsjerk! As far as I know .gro files are coordinate ones, containing the structure of the system. How is it possible to make difference between x,y and z AND vx,vy and vz? Should I write the file like coordinate format? Regards, Mah On Wed, Dec 24, 2014 at 7:44 PM, mah maz

Re: [gmx-users] initial velocities

Many thanks Tsjerk and Justin! You both helped alot. Regards, Mah On Wed, Dec 24, 2014 at 10:10 PM, mah maz mahma...@gmail.com wrote: Thank you very much Tsjerk! As far as I know .gro files are coordinate ones, containing the structure of the system. How is it possible to make difference

[gmx-users] extracting velocities

Dear all, What are the ways of extracting velocities from output files? I have used g_traj -f traj.trr -s topol.top but couldn't get the velocities. Are there any other commands to help me in this regard? Thank you! -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] extracting velocities

Thank you again Tsjerk! You mean -av all_veloc.xvg? Could you please tell me the differences between -cv veloc.pdb and the mentioned command? Regards ,Mah On Fri, Dec 26, 2014 at 10:05 AM, mah maz mahma...@gmail.com wrote: Dear all, What are the ways of extracting velocities from output

Re: [gmx-users] extracting velocities

Hi Tsjerk Got the point. It worked; thanks alot! Regards, Mah On Fri, Dec 26, 2014 at 12:23 PM, mah maz mahma...@gmail.com wrote: Thank you again Tsjerk! You mean -av all_veloc.xvg? Could you please tell me the differences between -cv veloc.pdb and the mentioned command? Regards ,Mah

[gmx-users] box siz

Dear all, I have calculated the size of the box required for my system. however, when applying the g_x2top command with this box size, a fatal error occurs: 'couldnt find forcefield for all atoms'. making the box larger in size, this error is not appeared. what is the exact problem; box size or

Re: [gmx-users] box siz

Hi Justin, Thank you! but what are the old and new box? I have defined only one box with editconf command. Regards, Mah On Tue, Dec 30, 2014 at 1:58 PM, mah maz mahma...@gmail.com wrote: Dear all, I have calculated the size of the box required for my system. however, when applying

Re: [gmx-users] box siz

Hi Justin, Yes, you are right! I think I know what to do now. Thank you very much! Regards, Mah On Wed, Dec 31, 2014 at 12:44 PM, mah maz mahma...@gmail.com wrote: Hi Justin, Thank you! but what are the old and new box? I have defined only one box with editconf command. Regards, Mah

Re: [gmx-users] atom freezing

, 2015 at 9:06 PM, mah maz mahma...@gmail.com wrote: Dear all, I want to have different situations for different atoms in my system. In the .mdp file how can I freez some of the atoms? ( I dont have residues in the system; 3 kinds of atoms are present just by one atom type name) Is it possible

[gmx-users] atom freezing

Dear all, I want to have different situations for different atoms in my system. In the .mdp file how can I freez some of the atoms? ( I dont have residues in the system; 3 kinds of atoms are present just by one atom type name) Is it possible to assign different situations to some of the atoms by

Re: [gmx-users] atom freezing

Dear Justin, Thank you for your help! Cheers, Mah On Thu, Jan 1, 2015 at 10:07 PM, mah maz mahma...@gmail.com wrote: Thanks Justin! I tried the freezegrps and freezedim but it needed the name of the groups. As I said in my system only one type of atom is defined. Should I put the desired

Re: [gmx-users] potential energy

not willing to reform from plane graphene system? I would appreciate your help. Many thanks in advance! Regards, Mah On Sun, Jan 11, 2015 at 5:31 PM, mah maz mahma...@gmail.com wrote: Hi Justin, That's right in the .edr I have more than these 4 terms, I just mentioned the terms related

Re: [gmx-users] potential energy

Dear Justin, Thank you very much for your beneficial analysis. The problem is not solved completely but the situation is improved for sure. Your help is always precious. Best Regards, Mah On 1/16/15, mah maz mahma...@gmail.com wrote: Hi Justin, I haven't come to a conclusion yet and need your

[gmx-users] msd calculation

Dear All, I want to calculate msd for a group of atoms of my system in different directions (x, y and z). What is the exact difference between -type, -lateral and -ten in g_msd command? which one should I use? Thank you! -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] coordinates file format

and confusing for me and the program both! According to your points, I can come to the conclusion that changing the file format is not possible. I appreciate your help as usual. thanks alot! Cheers, Mah On Mon, Jan 26, 2015 at 8:01 PM, mah maz mahma...@gmail.com wrote: Dear Mark, Thanks

Re: [gmx-users] coordinates file format

to read it in FORTRAN and I couldn't succeed! I'm not familiar with python. thanks anyway. Regards, Mah On Tue, Jan 27, 2015 at 12:31 PM, mah maz mahma...@gmail.com wrote: Dear Justin and Mark, I think you are both right. I didn't get your last sentence Mark! What is a libxdrfile? Justin

Re: [gmx-users] coordinates file format

Dear Mark, That was a great deal of help. This time, I agree with your last sentence ;-) Thanks a lot! Cheers, Mah On Wed, Jan 28, 2015 at 2:23 PM, mah maz mahma...@gmail.com wrote: Dear Mark, Erik Mark, thank you very much! I asked google and it didn't know either! ;-) your code also

Re: [gmx-users] coordinates file format

of the 1st atom and x2 y2 z2 are for the 2nd atom. Is it possible to get the file in a desired format? thank you! On Mon, Jan 26, 2015 at 11:54 AM, mah maz mahma...@gmail.com wrote: Dear all, I have extracted a file of coordinates after a simulation with 100 steps writen every 1000 steps

[gmx-users] coordinates file format

Dear all, I have extracted a file of coordinates after a simulation with 100 steps writen every 1000 steps, by g_traj -s -ox . The result is a file in which the first column is time and all coordinates are following it. Is there a way that I can get coordinates of each time step in a more

Re: [gmx-users] trash error in linux

Hi Mark, I have searched google for sure, but non of the solutions worked out except 'rm' which is a question cleaning remedy rather than solving the main problem! Thanks anyway, Mah On Tue, Jan 6, 2015 at 10:13 AM, mah maz mahma...@gmail.com wrote: Dear all, I have encountered a problem

[gmx-users] trash error in linux

Dear all, I have encountered a problem much related to linux not Gromacs. I wonder if anyone has seen this error before : trash has reached maximum size please clean manually while it is actually empty. any solutions? thank you! -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] potential energy

Thank you Justin! you mean we can have a stable system with positive potential and total energy? Regards, Mah On Sun, Jan 11, 2015 at 12:22 AM, mah maz mahma...@gmail.com wrote: Dear all, I wanted to know if the potential energy gained by g_energy -f ener.edr -o the total potential energy

Re: [gmx-users] potential energy

I see! You are right. But my system is a nanotube not in gas phase. Is it possible in this case? Thanks alot! On Sun, Jan 11, 2015 at 12:40 AM, mah maz mahma...@gmail.com wrote: Thank you Justin! you mean we can have a stable system with positive potential and total energy? Regards, Mah

[gmx-users] potential energy

Dear all, I wanted to know if the potential energy gained by g_energy -f ener.edr -o the total potential energy of the system or partial ones like vdw energy. If it is the total energy, to my knowledge it should be negative, and its summation with the kinetic energy should be negative showing the

Re: [gmx-users] potential energy

some solvent in nanotube actually! What do you mean by various energy components? In the results, I just have terms for potential, kinetic, total energy and conserved energy which are all positive in all steps. On Sun, Jan 11, 2015 at 12:52 AM, mah maz mahma...@gmail.com wrote: I see! You

Re: [gmx-users] potential energy

Hi Justin, That's right in the .edr I have more than these 4 terms, I just mentioned the terms related to energy of the system.The output file is a large one not in a proper format to be sent, but can be attached if possible. That was a great deal of help up to this point. Thank you very much!

[gmx-users] electric fields

Dear all, What kinds of electric and magnetic fields are available in gromacs? Are there any commands for discontinuous(alternating) fields? thank you! -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! *

Re: [gmx-users] electric fields

Hi all, I need to apply magnetic and also alternating electric field to my system, but I can't find any options. Can anyone help me? thanks! On Fri, Feb 13, 2015 at 8:44 PM, mah maz mahma...@gmail.com wrote: Dear all, What kinds of electric and magnetic fields are available in gromacs

Re: [gmx-users] electric fields

Dear Justin, David Thank you for your reply. I have also seen not implemented yet as Justin said. David, I hope your option E-xt works. But still I don't know if I should supply its parameters the same as E-x or it would be different. Thanks a lot! On Sun, Feb 15, 2015 at 9:01 PM, mah maz mahma

Re: [gmx-users] electric fields

, Feb 15, 2015 at 11:19 PM, mah maz mahma...@gmail.com wrote: Dear Justin, David Thank you for your reply. I have also seen not implemented yet as Justin said. David, I hope your option E-xt works. But still I don't know if I should supply its parameters the same as E-x or it would

Re: [gmx-users] trajectory film

Hi Justin, Thank you very much! On Thu, Mar 12, 2015 at 9:53 AM, mah maz mahma...@gmail.com wrote: Dear all, I have a question probably not related to this mailing list! I want to see a film of an output trajectory via VMD. I tried the .trr file by the appropriate format in VMD, it shows

[gmx-users] trajectory film

Dear all, I have a question probably not related to this mailing list! I want to see a film of an output trajectory via VMD. I tried the .trr file by the appropriate format in VMD, it shows that the frames are being constructed and rendering is complete but nothing can be seen. Is there a problem

Re: [gmx-users] forcefield error for atoms

be the solution? Thanks! On Mon, Mar 23, 2015 at 12:41 AM, mah maz mahma...@gmail.com wrote: Dear all, I need to insert some atoms (without any bonds to other atoms) or even ions in my system. I have created the .pdb, and .gro files, but when I try to generate the .top file it stops with the following

Re: [gmx-users] forcefield error for atoms

while making the topology file. How can I get rid of this error? Cheers! On Tue, Mar 24, 2015 at 9:00 PM, mah maz mahma...@gmail.com wrote: Hi Justin, Thanks for your reply. As you guessed correctly, for making a topology file I used g_x2top -f file.gro -o file.top -ff forcefield -noparam. I

Re: [gmx-users] high temperature

, 2015 at 10:08 PM, mah maz mahma...@gmail.com wrote: Hi Justin, So many thanks for your help. The problem was solved by changing cutoff to reaction-field-zero and epsilon_rf=0. It just may need some modifications for assigning right rvdw, rcoulomb and rlist. Thanks again! Cheers On Mon

Re: [gmx-users] high temperature

but don't know how to set them. Have you got any ideas to help? thanks! Cheers On Sun, Mar 1, 2015 at 8:55 PM, mah maz mahma...@gmail.com wrote: Dear Chaban, Thank you very much. Could you please explain more about the problem and how I may fix it? Cheers On Sun, Mar 1, 2015 at 11:16 AM, mah

Re: [gmx-users] high temperature

Hi Justin, So many thanks for your help. The problem was solved by changing cutoff to reaction-field-zero and epsilon_rf=0. It just may need some modifications for assigning right rvdw, rcoulomb and rlist. Thanks again! Cheers On Mon, Mar 2, 2015 at 7:03 PM, mah maz mahma...@gmail.com wrote

Re: [gmx-users] high temperature

at 10:30 PM, mah maz mahma...@gmail.com wrote: Dear Justin, You are right, but I'm not asking about conditions in .mdp. I wanted to ask how a result(of temperature here) can be different from one computer to another while I have even the same GROMACS versions in both? I copied the .gro .top .mdp

Re: [gmx-users] high temperature

results to another, but I see about 150K difference in temperature! Your help is greatly appreciated. Thanks! On Tue, Mar 3, 2015 at 10:41 AM, mah maz mahma...@gmail.com wrote: Hi Justin, I performed the run with the reaction-field-zero as I said, but when I try to simulate it with exactly

[gmx-users] high temperature

Dear all, I have a CNT system. I have set the mdp file as follows, but the temperature output is logically more than what I expected even in the production step(around 500k). I have changed the mdp file several times but it doesn't work. What are the possible causes of problem? Thank you! dt

Re: [gmx-users] high temperature

Dear Chaban, Thank you very much. Could you please explain more about the problem and how I may fix it? Cheers On Sun, Mar 1, 2015 at 11:16 AM, mah maz mahma...@gmail.com wrote: Dear all, I have a CNT system. I have set the mdp file as follows, but the temperature output is logically more

Re: [gmx-users] several runs

Hi Justin, Thank you for your answer! If you may help with any of these questions I would be greatly grateful; How can I understand if they were interfered? How is pinning? Any other ways you can recommend? Thanks a lot On Tue, Feb 24, 2015 at 10:14 PM, mah maz mahma...@gmail.com wrote

Re: [gmx-users] several runs

Is running simulations in several terminals problematic? On Tue, Feb 24, 2015 at 8:42 PM, mah maz mahma...@gmail.com wrote: Dear all, How can I perform several simulations simultaneously (in linux)? thank you! -- Gromacs Users mailing list * Please search the archive at http

[gmx-users] several runs

Dear all, How can I perform several simulations simultaneously (in linux)? thank you! -- 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 *

Re: [gmx-users] several runs

Dear Mark,Victor,Szilard So many thanks for your helpful comments! Cheers On Tue, Feb 24, 2015 at 11:10 PM, mah maz mahma...@gmail.com wrote: Hi Justin, Thank you for your answer! If you may help with any of these questions I would be greatly grateful; How can I understand if they were

[gmx-users] atom freezing during simulation

Dear all, I need to freeze some atoms in my system not to move during simulation. I used freezegrps and freezdim options but after simulation, I can see that the fixed atoms also moved and their coordinates changed. What can I do to fix their positions? Should I couple them with thermostat and

Re: [gmx-users] RDF

Thanks Justin! I cant find so much details in the manual; there are only general facts. does g_density give partial density? On Mon, May 18, 2015 at 11:25 AM, mah maz mahma...@gmail.com wrote: Hi Justin The fact is I want to calculate water density in the system. If I select group1: oxygen

Re: [gmx-users] RDF

? Thanks a lot! On Sun, May 17, 2015 at 2:17 PM, mah maz mahma...@gmail.com wrote: Dear all, I want to calculate the radial distribution function of water molecules in my system. I use g_rdf -f traj.xtc -n -o. It gives me large numbers which is not logical I suppose. Is it meaningful if I

[gmx-users] RDF

Dear all, I want to calculate the radial distribution function of water molecules in my system. I use g_rdf -f traj.xtc -n -o. It gives me large numbers which is not logical I suppose. Is it meaningful if I separate oxygen and hydrogen atoms in the index file and calculate the RDF for O-O atoms?

Re: [gmx-users] forcefield error for atoms

the inserted atoms for the pure CNT system. changes in the .n2t file were also considered including atom introduction. It worked! Cheers On Thu, Mar 26, 2015 at 1:34 PM, mah maz mahma...@gmail.com wrote: Hi Justin, Thank you! I checked the coordinates and I think there's nothing wrong with them

[gmx-users] simultaneous runs

Dear all, I performed 2 runs one after the other. Then, I performed those 2 runs simultaneously(no special commands were applied, I just used different terminals with mdrun -v command) but in different directories. Results (like msd and energies) were expected to be nearly the same. but they are

Re: [gmx-users] simultaneous runs

Thank you very much Justin! it was helpful as usual. On Sun, Apr 5, 2015 at 9:40 AM, mah maz mahma...@gmail.com wrote: Dear all, I performed 2 runs one after the other. Then, I performed those 2 runs simultaneously(no special commands were applied, I just used different terminals

Re: [gmx-users] installation errors

questions now: is it ok not to have gromacs installed in root? when I want to run is it necessary to have the file in the directory installed? and does double precision work the same as single?(I can see _d after commands) thanks alot On Mon, Jun 22, 2015 at 11:14 PM, mah maz mahma...@gmail.com

Re: [gmx-users] installation errors

Thanks Parvez! but it was not the solution. do you have any other ideas to help? On Sun, Jun 21, 2015 at 1:42 PM, mah maz mahma...@gmail.com wrote: Dear all, I am trying to install a new version of gromacs(rather than rpm) on my system. I apply these commands:(in root while im superuser) tar

[gmx-users] installation errors

Dear all, I am trying to install a new version of gromacs(rather than rpm) on my system. I apply these commands:(in root while im superuser) tar -xzvf fftw-3.3.4.tar.gz cd fftw-3.3.4 ./configure --enable-float --enable-threads make make install and for gromacs: tar -xzvf gromacs-4.5.5.tar.gz cd

Re: [gmx-users] .mdp parameters source codes

It worked Justin. So many thanks! In the RPM version there is a lack of these source codes. Can I copy them from other versions? Cheers! On Sat, Jun 13, 2015 at 11:17 PM, mah maz mahma...@gmail.com wrote: dear all, I really need to know where i can find files that are written in C format

Re: [gmx-users] files related to commands in C or FORTRAN

hi Justin, in the gromacs website i can see different versions, regressiontests and xdrs. which one should i download? my question is about a code written for each command eg. msd calculation. where can i find it? thank you! On Fri, Jun 12, 2015 at 11:06 PM, mah maz mahma...@gmail.com wrote

Re: [gmx-users] files related to commands in C or FORTRAN

Thank you very much Justin, Stephane. I found them. Where can I find .mdp parameters related files eg. thermostat code or electric field? On Fri, Jun 12, 2015 at 11:27 PM, mah maz mahma...@gmail.com wrote: hi Justin, in the gromacs website i can see different versions, regressiontests

[gmx-users] .mdp parameters source codes

dear all, I really need to know where i can find files that are written in C format for .mdp parameters like thermostat, cutoffs and electric fields. I searched in the source files and couldnt find anything. can anyone help me? thanks! -- Gromacs Users mailing list * Please search the archive at

[gmx-users] files related to commands in C or FORTRAN

dear all, i want to find files that are probably written in C, C++ or fortran format for commands in gromacs. i tried root/usr/share/gromacs but there are only a few files, not all of them. note that the version i installed is a rpm one. where can i find them? thanks! -- Gromacs Users mailing

[gmx-users] calculating electric field force

Dear all, I want to calculate the force caused by applying electric field in my system. I used g_traj -f tarj.xtc -of but it doesn't work. Does -of give external force? Are there any options to calculate the force from electric field? Thank you! -- Gromacs Users mailing list * Please search the

[gmx-users] segmentation fault

Dear all, for applying electric field in gromacs-4.5.5 I should enter 3 numbers. The first one is number of cosines that should be 1. any number smaller than 1 is acceptable but when I use 1, grompp is done but mdrun doesnt start with the following error: segmentation fault. What should I do? Is

[gmx-users] segmentation fault

Dear all, what is the solution for the segmentation fault after applying electric field? when I enter 1 for number of cosines mdrun doesnt start with segmentation fault error. does it mean that i can write any numbers as number of cosines and have stationary electric field or should i enter 1

Re: [gmx-users] PBC

I thought so :D Thanks! On Thu, Oct 8, 2015 at 9:37 AM, mah maz <mahma...@gmail.com> wrote: > Hi Mark > > Thank you. I suppose grid can be used without PBC specially when the > system is in vacuum. > There are some parameters in the .mdp file that I haven't defined an

Re: [gmx-users] PBC

, Do they play a role in the simulation? Thanks! On Mon, Oct 5, 2015 at 2:26 PM, mah maz <mahma...@gmail.com> wrote: > Hi Mark, > Thanks. It seems the default is pbc =xyz. But my question is if I don't > use PBC, can I use grid, or grid is only meaningful when PBC is defined? &g

[gmx-users] topology parameters

Dear users, Are resnr, residue, moleculetype, system and molecules names in .top file important? I have a CNT containing water molecules. I can see weather I assign CNT to all the molecules as residue names Or CNT and water, results are the same. Also if I use 1 for CNT as resdnr and 2 for water

[gmx-users] PBC

Dear users, If I dont define pbc=no, what is the default type for gromacs? Is it right if I dont use pbc=no in my system while using grid for ns-type? thank you. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before

Re: [gmx-users] PBC

Hi Mark, Thanks. It seems the default is pbc =xyz. But my question is if I don't use PBC, can I use grid, or grid is only meaningful when PBC is defined? On Mon, Oct 5, 2015 at 11:07 AM, mah maz <mahma...@gmail.com> wrote: > Dear users, > > If I dont define pbc=no, what is t

Re: [gmx-users] extracting coordinates from traj.xtc

And also, if I want velocities for every step what can I do? Thanks! On Sun, Dec 6, 2015 at 11:19 AM, mah maz <mahma...@gmail.com> wrote: > Thank you. I tested gmxdump and also trjconv -dump and compared traj.trr > and traj.xtc. You are right both have the same data.

Re: [gmx-users] extracting coordinates from traj.xtc

time consuming. And I couldn't find a way yet! Is there a command like g_traj -f traj.trr -ox to print coordinates from traj.xtc? Thanks! On Thu, Dec 3, 2015 at 8:27 PM, mah maz <mahma...@gmail.com> wrote: > Thanks Justin! I checked the run and it seemed ok. The fact is, the data I > g

[gmx-users] extracting coordinates from traj.xtc

Dear all, I have some problems extracting data from traj.xtc. The command " g_traj -s -ox" doesn't give reasonable coordinates. I tried "trjconv" but again couldn't get any results. Note that I have nstxtcout = 1 and xtc_grps = water in my .mdp file. Any help is appreciated. Thank you! --

Re: [gmx-users] extracting coordinates from traj.xtc

Thank you Justin. I expected that only water molecules are written in .xtc but all the others are there! g_traj -f traj.xtc -ox gives numbers like 1.64e-318 for all frames! How can I get real coordinates from .xtc? Thanks! On Tue, Dec 1, 2015 at 10:34 AM, mah maz <mahma...@gmail.com>

Re: [gmx-users] a suitable forcefield for ions

Thanks Erik. I found nonbonded parameters for atoms only in Amber ff. Can I use them for ions or they are already for ions? eg. for Na sigma= 0.332 and epsilon=0.0115. Does it mean that we can use thIS sigma and epsilon for Na+? On Wed, May 25, 2016 at 2:11 PM, mah maz <mahma...@gmail.com>

Re: [gmx-users] a suitable forcefield for ions

Thanks Justin. I can only find atoms in ffnonbonded.itp in Amber ff. Where should I search for ions parameters in Amber ff? On Wed, May 25, 2016 at 4:01 PM, mah maz <mahma...@gmail.com> wrote: > Thanks Erik. I found nonbonded parameters for atoms only in Amber ff. Can > I use t

Re: [gmx-users] Electric field unit

Thank you David but it still seems conflicting to me. V/nm and V/m are 100 times different! If it is in V/nm then force unit should be wrong! On Thu, Jan 14, 2016 at 12:20 PM, mah maz <mahma...@gmail.com> wrote: > Hi David, > > In the manual 4.6.7, Page8. It seems logical since

[gmx-users] necessary input files during simulation

Dear users, I deleted my input files(.gro,.mdp,.top,.ndx..) before the simulation is over by mistake. However, it is still running. Which files should be present to the end of a run? Thank you. -- Gromacs Users mailing list * Please search the archive at

[gmx-users] Electric field unit

Dear users, What is the electric field unit in gromacs? In the manual it is KJ/mol.nm.e but in the source code I encountered V/nm which is about 100 times KJ/mol.nm.e. Thank you. -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] necessary input files during simulation

Hi Tsjerk, Thank you very much. On Thu, Jan 14, 2016 at 10:46 AM, mah maz <mahma...@gmail.com> wrote: > Dear users, > > I deleted my input files(.gro,.mdp,.top,.ndx..) before the simulation is > over by mistake. However, it is still running. Which files should be > presen

Re: [gmx-users] Electric field unit

Seems rational! Thank you very much David. On Thu, Jan 14, 2016 at 7:20 PM, mah maz <mahma...@gmail.com> wrote: > Thank you David but it still seems conflicting to me. V/nm and V/m are 100 > times different! If it is in V/nm then force unit should be wrong! > > On Thu, Jan 14

[gmx-users] a suitable forcefield for ions

Hi all, i need forcefield parameters for ions. can anyone tell me which forcefield contains ions? can i do ion simulations with amber ff? Thank you -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't