Hi all.<br><br>Well, I'm having a great problem in some NpT simulations I'm running here, which leaded me to some concerns. Let me try to explain the situation:<br><br>Ok, I know: everywhere, including this list, amber list and any computational chemistry list informs that the compressibility of the liquid doesn't really matters for the NpT simulations, it will just change the "response time" of the system.
<br><br>Knowing that, I've started to make some simulations on a new system here: CF4. NVT equilibration, box in the proper volume, 500 molecules. After long time, change to Parrinello-Rahman barostat. Almost blowed, but came back as fast as almost were lost.
<br><br>I was using tau_p of 0.400 and compressibility of 116 e-6 (not even I remember where that came from). The target volume is 45.66nm**3 at 123K and 1 atm. The potential is from AMBER, and is properly written in the topology files (reverified that about a thousand times).
<br><br>The system kept going to a average volume around 53.4 nm**3, didn't matter whatever I did with the simulation parameters. The reproducibility, from the original Kollman's paper, show's that there should be about 1-2% deviation. I kept trying for about 1ns of simulation, couldn't be more stable (it would be great if it was in the correct value!).
<br><br>After all reverifications possible, I decided to change exactly what is supposed to not alter this property: compressibility. I lowered it from 11.6e-5 to 4.5e-5.<br><br>The volume reacted with an immediate drop to 50nm**3.
<br><br>I did not yet tried to change parrinello for berendsen. By now, I'm dealing with the tau_p increase, from 0.400 to 0.700, which also yelded me an reduction from 50nm**3 to 49-49.5nm**3. This means that it's not big deal to change the tau_p, what is also interesting since amber official and original guidelines uses the
0.400 ps coupling for pressure (only that with the nosè barosthat).<br><br>The points I'm questioning here now is:<br><br>1 - Is the compressibility of the system a value that basically should "not matter" what I put in there?
<br><br>2 - to what range is this "not matter" related?<br><br>3 - I'll keep trying the compressibility, and see if will reach at some value the expected volume. The question now is, will it reach any point acceptable? And after this point, will it be still stable, start to grow the volumes again, or will just keep falling (worst scenario)?
<br><br>4 - since it should not affect the simulated property... what's happening here, in such a way that it IS affecting the simulated property?<br><br>I'm really sorry if this is any kind of obvious subject, but I really tried to find any different reason for these observations. Could not find nothing related in any list, including this one. So I thought about taking the facts to the discussion list and see what appears.
<br><br>Thanks in advance for anyone and any answer!<br><br>Sincerally yours,<br><br>Jones<br>