[gmx-users] TIP4P water model

[Peter C. Lai]

Perhaps genion is not removing the dummy atoms properly?

On 2012-09-21 04:48:37PM +0100, Ankita naithani wrote:
> Hi all,
> 
> I am trying to begin a simulation of a protein.
> 
> I am using AMBER99sb-ILDN force field and TIP4P water model. However,
> I am facing a problem in the ion adding step.
> 
> when  I issue the grompp command to generate the necessary .tpr file
> for simulation to be utilised by genion tool, I get the following
> error :
> 
> "Fatal error:
> number of coordinates in coordinate file (system_solv.gro, 421880)
>              does not match topology (topol.top, 416008)
> "
> 
> However, I have rechecked several times my topology file and the
> co-ordinate file and I am running it pretty straightforward to get
> this error. When I try TIP3P water model for the same protein, I do
> not get the error.
> 
> I get the same error when I use TIP4P-Ew water model too. I have
> decide a better water model for my system before I run my final
> production simulations and so I have been trying to compare both the
> water models. I am wondering if anyone could kindly suggest the
> possible reason for this error because ideally, it should not be
> giving me any error at this stage as I haven't manipulated with
> anything.
> 
> I am also appending my ions.mdp info below:
> 
> ; ions.mdp - used as input into grompp to generate ions.tpr
> ; Parameters describing what to do, when to stop and what to save
> integrator	= steep		; Algorithm (steep = steepest descent minimization)
> emtol		= 1000.0  	; Stop minimization when the maximum force < 1000.0 kJ/mol/nm
> emstep          = 0.01          ; Energy step size
> nsteps		= 50000	  	; Maximum number of (minimization) steps to perform
> 
> ; Parameters describing how to find the neighbors of each atom and how
> to calculate the interactions
> nstlist		= 1		; Frequency to update the neighbor list and long range forces
> ns_type		= grid		; Method to determine neighbor list (simple, grid)
> rlist		= 0.9		; Cut-off for making neighbor list (short range forces)
> coulombtype	= PME		; Treatment of long range electrostatic interactions
> rcoulomb	= 0.9		; Short-range electrostatic cut-off
> rvdw		= 0.9		; Short-range Van der Waals cut-off
> pbc		= xyz 		; Periodic Boundary Conditions (yes/no)
> 
> -----------
> 
> 
> 
> -- 
> Ankita Naithani
> -- 
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-- 
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Peter C. Lai			| University of Alabama-Birmingham
Programmer/Analyst		| KAUL 752A
Genetics Div. of Research	| 705 South 20th Street
pcl at uab.edu			| Birmingham AL 35294-4461
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