[gmx-users] TIP4P water model

[Justin Lemkul]

On 9/21/12 7:55 PM, Peter C. Lai wrote:
> Perhaps genion is not removing the dummy atoms properly?
>

The problem is occurring with grompp before genion.  We would need to see all 
the prior commands (exactly copied and pasted from the terminal) as well as the 
[molecules] section of the topology, to at least start to guess at what's wrong. 
  It is unusual to find a failure in grompp before genion.

-Justin

> 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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-- 
========================================

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

========================================