AMBER Archive (2006)

Subject: Re: AMBER: restraints and constant pressure

From: Joshua (
Date: Fri Oct 13 2006 - 17:46:26 CDT

Thanks very much for everyone's replies on the constant pressure issue. I just tried the technique suggested by Dr. Cheatham, in which the prmtop file was altered to merge the molecules (49 different molecules in this case) into a single molecule. I followed the directions from the "AMBER: ibelly problem" coversation in the AMBER archive. (This involved changing the ATOMS_PER_MOLECULE section to reflect the new molecule division, changing the total number of molecules, and changing the first solvent molecule. I made no other changes.) When I tried to run a job using this prmtop file, sander appeared to read the prmtop file without complaints--here's a section from the .out file:

| New format PARM file being parsed.
| Version = 1.000 Date = 08/28/06 Time = 20:35:50
 NATOM = 215513 NTYPES = 22 NBONH = 194471 MBONA = 21203
 NTHETH = 46375 MTHETA = 28777 NPHIH = 87282 MPHIA = 61432
 NHPARM = 0 NPARM = 0 NNB = 459238 NRES = 60969
 NBONA = 21203 NTHETA = 28777 NPHIA = 61432 NUMBND = 63
 NUMANG = 134 NPTRA = 73 NATYP = 42 NPHB = 1
 IFBOX = 1 NMXRS = 39 IFCAP = 0 NEXTRA = 0
 NCOPY = 0

However, the job then crashed before completing any steps, with the following message in the .in.err file:

[3] MPI Abort by user Aborting program !
forrtl: error (76): IOT trap signal
prun: no core file to analyse
prun: no core file to analyse

I strongly suspect that I have just made a mistake in my input file, but I am stumped as to what the problem could be. Here is the input file:

  restraintmask=':1-382, 2293-2674',

Does anyone have any suggestions on what might be wrong with the input file, or a mistake that I could have made in altering the .prmtop?

Thank you very much for your help.


 --- On Fri 09/15, Thomas Cheatham < > wrote:
From: Thomas Cheatham [mailto:]
Date: Fri, 15 Sep 2006 00:22:02 -0600 (Mountain Daylight Time)
Subject: Re: AMBER: restraints and constant pressure

> "Using constant pressure with restraints can also cause problems so > initially we will run 20 ps of MD at constant volume."> > I am working with a system where it is really necessary to use > restraints on about one third of the solute. I had planned on using > ntr=1 with a force constant of 10 kcal/mol. Could someone please specify > what the risks are of combining restraints with constant pressure, and > how I can minimize those risks?At issue is that pressure scaling works by shifting (scaling) the relative positions of each molecule (in older versions when NPSCAL=1 or atoms when NPSCAL=0) in the box to increase or decrease the size.To simplify the restraint code, rather than inducing a force (coordinate deviation) every time the simulation coordinates are scaled (relative to the restraint coordinates), it was decided to scale the restraint coordinates as well. This effectively changes the restraint coordinates at each step (every time the coordinates are scaled). Tw!
problems may result:(1) when you restart, and reference previous restraint coordinates (that were not shifted), you will get an initially large restraint energy due to the "shift", and(2) if you are restraining multiple molecules, the relative positions of the molecules will change as the simulation proceeds. Imagine the default case where the density of the water is too low initially, the box has to contract. If you are restraining two molecules, for example the two strands of DNA, as the run continues, the restraint coordinates will shift the molecules closer together which will force your MD coordinates to cause the two strands to get closer. This is undesirable.In the older DNA tutorial, a discussion was present that provided this info; to get around (2), I normally edit the prmtop file to coalesce the first two molecules (i.e. two strands of DNA for example) into a single molecule (and change the pointers to reflect this).To get around (1), I normally use the restrt
file as the refc coordinates for a continuation...So, short summary: if you are restraining a single molecule (like a single protein chain), you likely will not suffer serious artifact and can get away with shifting (as per (1) above) noting that upon restart the restraint energy will be a little higher than expected due to the shifting. As long as the force constant for NTR is not too high (1.0 kcal/mol is often strong enough a restraint), this shift should not lead to integration failure.I hope this helps,--tom-----------------------------------------------------------------------The AMBER Mail ReflectorTo post, send mail to amber_at_scripps.eduTo unsubscribe, send "unsubscribe amber" to

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