Re: [gmx-users] genion command

[Justin Lemkul]

On 5/16/17 12:55 AM, Saumyak Mukherjee wrote:

Hello Diana,

You may try using the -conc flag in genion program to specify your salt
concentration, along with -nname and -pname flags.



The -nname and -pname options are irrelevant here.

If there are fewer than 1000 waters in the system, I doubt the number of ions 
has been calculated correctly, though.  Compare with -conc 0.6 to see if the 
math is right, and make sure that the solvent is actually being replaced, not 
anything else.


-Justin


Best wishes,
Saumyak

On 16 May 2017 at 10:18, diana p  wrote:


Dear gmx users,
I want to simulate 0.6M CaCL2 aqueous solution. To add the ions I use
genion command and add 720 CL and 360 Ca ions respectively to the system of
pure 12568 water molecules.But on running the command genion I get error
message:

Program genion, VERSION 4.6.5
Source code file: /build/buildd/gromacs-4.6.5/src/tools/gmx_genion.c,
line:
89
Fatal error:
No more replaceable solvent!

How should I add ions in the system.I would be more than pleased if someone
could guid me.
Thank You in advance
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--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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Re: [gmx-users] genion command

[Saumyak Mukherjee]

Hello Diana,

You may try using the -conc flag in genion program to specify your salt
concentration, along with -nname and -pname flags.

Best wishes,
Saumyak

On 16 May 2017 at 10:18, diana p  wrote:

> Dear gmx users,
> I want to simulate 0.6M CaCL2 aqueous solution. To add the ions I use
> genion command and add 720 CL and 360 Ca ions respectively to the system of
> pure 12568 water molecules.But on running the command genion I get error
> message:
>
> Program genion, VERSION 4.6.5
> Source code file: /build/buildd/gromacs-4.6.5/src/tools/gmx_genion.c,
> line:
> 89
> Fatal error:
> No more replaceable solvent!
>
> How should I add ions in the system.I would be more than pleased if someone
> could guid me.
> Thank You in advance
> --
> 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-requ...@gromacs.org.
>



-- 

*Saumyak Mukherjee*

Junior Research Fellow
Prof. Biman Bagchi's Group
Solid State and Structural Chemistry Unit
Indian Institute of Science
Bangalore - 560012

Mob : 8017292426
Alternative e-mail : saumyakmukher...@gmail.com
smukher...@sscu.iisc.ernet.in

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Re: [gmx-users] Genion command not working

[srinivasa rao lanke]

Thank you very much your reply
its working fine if i decrease distance

thank you

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