[gmx-users] TIP4P water model
jalemkul at vt.edu
Sat Sep 22 01:57:38 CEST 2012
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.
> 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
>> 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.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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