Hello Carlos and David,
Thank you very much for suggestions. I tried your suggestion by using a buffer of 8 with the solvate command. It worked but added extra 1600 plus water molecules to my system. I used to sanders do perform several equilibration to a density of 1.1037 close to the target density of 1.1567 and then I switched to cuda which worked albeit slow process. Is the data generated reliable? Since I have modified/generated water model through a process not as rigorous as suggested by Carlos. I must add that this challenge is not limited to a complex system like water-ionic liquid-cellulose-ethanol , I encounter the same problem when am even simulating a simple system like cellulose-ionic liquid mixture.
Another challenge is that my system does not seem to have any intermolecular hydrogen bonding between either ionic liquid ions and cellulose or cellulose and water after simulation as expected. It is only intramolecular hydrogen bonding between hydroxyl groups of cellulose that cpptraj sees in my system, both in ionic liquid -cellulose mixture and ionic liquid-cellulose water. I have attached the hydrogen bond command here:
cpptraj.hbond.in
parm ionicbox2.prmtop
trajin prod3_md.nc
hbond contact ': 'AMI', ':ROH, 0GB, 4GB' avgout avg.dat series uuderies hbond.gnu nointramol
go
lifetime contacts[solutehb] out contactr-lifetime.dat
Please kindly tell what is wrong with my script or if the problem emanates from wrong input script I used am ready to supply them. Thank you
Alex
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Received on Fri Apr 09 2021 - 10:00:02 PDT
