GROMACS version:2022.1
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Dear all,
I am trying to run a simple water simulation using the TIP4P/2005 model with AmberGS forcefield. I have got the tip4p_2005.itp but I am unable to understand how can we get the initial .gro file for the simulation. For simple Tip4p, the .gro file is already present in the top folder. Any assistance in this regard is highly appreciated.
Thank you.
Dear @Abhi1
You can use gmx solvate to create the starting box. The water models you have to choose in the tool are in the installation directory of GROMACS, something like /path-to-gromacs-install-directory/share/gromacs/top/. There you will find topology and structure file for various water models, including TIP4P.
Dear @obZehn,
Thank you so much for your kind reply. In the top folder, structure files for TIP4P model are present but not for the TIP4P/2005 model. There is some geometrical difference in structure between TIP4P and TIP4P/2005 and as per my understanding so far, we cannot take the TIP4P .gro file when using TIP4P/2005 water model.
Dear @Abhi1
In this case then I am sorry I am not able to tell you where to find the specific .gro file. However, as long as you have the topology, I feel like whatever difference between the different models will be washed out by a few ps of run.
Thanks again dear @obZehn, I also thought the same thing. I am just not sure about the correctness of this approach.
The geometry will be fixed at step 0 of the energy minimization or an MD simulation. The liquid structure might differ by a very small amount, but that’s irrelevant when you are anyhow equilibrating for least a few ps.
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Thank you so much dear @Hess for your kind help. My confusion is now completely resolved.