Re: [gmx-users] Simulation of Small Water Box

[Justin Lemkul]

On 5/3/13 5:41 AM, Monoj Mon Kalita wrote:

Dear Users

Can Anybody help me to simulate a water box with nearly 14.45 A  box size
and approximately 93 water molecules. I have tried to simulate it using the
'spc' water model. I have done the SD and CG minimization step. Till that
step it was fine, but when I tried to do MD then I got the following error
message

*One of the box vectors has become shorter than twice the cut-off length or
box_yy-|box_zy| or box_zz has become smaller than the cut-off.*

Is there any well established method to simulate a small water box nearly
of the size I have mentioned? It would be great if I could get it. Have a
nice day.



The error warns you that you are violating the minimum image convention.  For a 
system of such a tiny size, fluctuations in the box vectors that arise from 
pressure coupling can be quite significant.  Unless you are using a cutoff of 
0.7 nm or less (which would be incorrect to do, as you will have serious cutoff 
errors), you cannot use a box this small.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] Simulation of Small Water Box

[Monoj Mon Kalita]

Dear Users

Can Anybody help me to simulate a water box with nearly 14.45 A  box size
and approximately 93 water molecules. I have tried to simulate it using the
'spc' water model. I have done the SD and CG minimization step. Till that
step it was fine, but when I tried to do MD then I got the following error
message

*One of the box vectors has become shorter than twice the cut-off length or
box_yy-|box_zy| or box_zz has become smaller than the cut-off.*

Is there any well established method to simulate a small water box nearly
of the size I have mentioned? It would be great if I could get it. Have a
nice day.

-- 
With Regards
Monoj Mon Kalita
Institute of 
Biophotonics
National Yang-Ming University
Taipei, Taiwan
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists