[gmx-users] the study of concentration effect in gromacs

Tsjerk Wassenaar tsjerkw at gmail.com
Sat Apr 4 21:48:11 CEST 2015

Hi Elham,

No, a box of 0.5*0.5*0.5 has 0.125 times the volume of one of 1*1*1, so
gives an 8 times as high concentration. But it gets more complicated if you
mean the concentration of the solution around a protein. I tend to favour
using molality (as mol solute per mol solvent) for that.

Yes, you'll need to merge the coordinates.

What do you mean "Aspirin with Salicilic Acid"? Aspirin is acetylated
salicylic acid.



On Sat, Apr 4, 2015 at 8:36 PM, elham tazikeh <elham.tazikeh at gmail.com>

> Dear Tsjerk
> thanks for your advice
> you mean , if i do my simulation in cubic box (1*1*1  nm3)...
> Now, for twice of concentration, i should simulate for example in cubic box
> (0.5*0.5*0.5  nm3)?
> or for instance, i simulated on a system using *2i30* pdb file
> (Aspirin+Salicilic Acid)
> that including 2 molecules Aspirin with Salicilic Acid.
> for increasing the concentration of substrate in this system, how can i
> insert 2 molecules Salicilic Acid?i must insert the coordinate of Salicilic
> Acid in my pdb file, again or not?
> cheers
> --
> 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)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.

Tsjerk A. Wassenaar, Ph.D.

More information about the gromacs.org_gmx-users mailing list