[AMBER] Problem with Phenylphosphonic acid

From: Gustaf Olsson <gustaf.olsson.lnu.se>
Date: Fri, 12 Jul 2019 13:15:34 +0000

Hello amber community

I now return with a simulation problem as opposed to the software issues I am usually nagging about.

I am running three different systems that contain pehnylphosdhonic acid, the neutral form (ppa) the anion (pp1) and the double negative anion (pp2).

These are being simulated in a tetrahydrofuran box with cations to adjust to zero charge. Now, I noticed that all the systems containing the neutral form (ppa) crashed with either a segmentation fault or a vlimit exceeded problem after just a few iterations, in most cases less than 2000 iterations, meaning I had basically no output to look at.

The systems containing the charged ion forms of ppa (pp1 and pp2) seems to be running OK so far and I cannot figure out what is wrong with the structure I have for ppa. I have recalculated the charges using both AM1 and gaussian RESP and they are comparable. I have checked the things I usually get wrong and none of them seem to be incorrect. The structure is correct, the charges look reasonable and are comparable between methods so if this was the problem both methods perform equally poor. I get no complaints from antechamber or xleap when setting up the simulations and the energy minimisation seems to work, at least for the test systems I have run.

I ended up putting just 1 ppa molecule in a box with 1500 solvent molecules using tetrahydrofuran, dmso and acetonitrile. They all crash with the vlimit error when using sander and seg.fault. with pmemd. Obviously something is moving way to fast and looking at the few frames of output I managed to get with the dmso solvent box this molecule does move however I cannot see any truly "unnatural” motions as I have observed before. Running just the solvents does not cause any of these problems.

I realise what the problem is, something is moving way to fast and in a non-describable manner. However I find myself unable to identify a cause for the observed behaviour.

I am attaching the pdb/prepi/frcmod files generated hoping that someone else might be able to tell me that I just made some dumb mistake because otherwise I am at a loss as how to simulate these systems.

Let me know if anything else is needed and thank you in advance

Best regards
// Gustaf

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Received on Fri Jul 12 2019 - 06:30:04 PDT
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