Re: [gmx-users] water molecule cannot be settled during minimization!!!!

[Wes Barnett]

On Mon, Nov 6, 2017 at 12:17 AM, Seera Suryanarayana 
wrote:

> Dear gromacs users
>
> I am trying to simulate one protein with 180 residues. During energy
> minimization I got the falling error.
>
> Fatal error:
>
> step 26: Water molecule starting at atom 28787 can not be settled.
> Check for bad contacts and/or reduce the timestep if appropriate.
>
> I have reduced the em step size from 0.01 to 0.02  as I got this suggestion
> from archives. I  still have the same problem. I request you to give a
> suggestion how to resolve it.
>

You went the wrong direction and increased the size of the time step,
unless that is a typo.


>
> Thanks in advance
> Surya
> Graduate student
> India.
>



-- 
James "Wes" Barnett
Postdoctoral Research Scientist
Department of Chemical Engineering
Kumar Research Group 
Columbia University
w.barn...@columbia.edu
http://wbarnett.us
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Re: [gmx-users] water molecule cannot be settled during minimization!!!!

[Vytautas Rakeviius]

Investigate same water molecule mentioned in error in vmd or such program 
likely it is in close contact to other molecule.You can move it manually by 
altering coordinates in gro text file into more realistic starting position.Or 
probably even better if you redo your solvatation again (with different 
parameters?).
 

On Monday, November 6, 2017, 7:18:18 AM GMT+2, Seera Suryanarayana 
 wrote:  
 
 Dear gromacs users

I am trying to simulate one protein with 180 residues. During energy
minimization I got the falling error.

Fatal error:

step 26: Water molecule starting at atom 28787 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

I have reduced the em step size from 0.01 to 0.02  as I got this suggestion
from archives. I  still have the same problem. I request you to give a
suggestion how to resolve it.

Thanks in advance
Surya
Graduate student
India.
-- 
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Re: [gmx-users] water molecule cannot be settled during minimization!!!!

[Dallas Warren]

Visualise the system and check where the water is located and the atoms
surrounding it.

On 6 Nov. 2017 4:18 pm, "Seera Suryanarayana"  wrote:

Dear gromacs users

I am trying to simulate one protein with 180 residues. During energy
minimization I got the falling error.

Fatal error:

step 26: Water molecule starting at atom 28787 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

I have reduced the em step size from 0.01 to 0.02  as I got this suggestion
from archives. I  still have the same problem. I request you to give a
suggestion how to resolve it.

Thanks in advance
Surya
Graduate student
India.
--
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Support/Mailing_Lists/GMX-Users_List before posting!

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[gmx-users] water molecule cannot be settled during minimization!!!!

[Seera Suryanarayana]

Dear gromacs users

I am trying to simulate one protein with 180 residues. During energy
minimization I got the falling error.

Fatal error:

step 26: Water molecule starting at atom 28787 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

I have reduced the em step size from 0.01 to 0.02  as I got this suggestion
from archives. I  still have the same problem. I request you to give a
suggestion how to resolve it.

Thanks in advance
Surya
Graduate student
India.
-- 
Gromacs Users mailing list

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