Hello, thank you for your help.
I will try without counter ions only then, and see if I can get the
information I want this way.
I will follow the advice from Carlos and use igb=8 with mbondi3, with
ff14SB.
I am using sander.MPI and I am running in this way:
mpirun -np X sander.MPI -O -i mdin -o mdout -p prmtop -c inpcrd -r rst -x
mdcrd
where X has been either 8 or 16.
I am new to amber so I haven't tried pmemd, but I will do it soon.
May I be limited to 8 processors also in MD?
I am also simulating the same peptide in TIP3PBOX solvent. So far I haven't
had problems running it on 16 processors. Could I encounter the same
problems with this simulation with explicit solvent?
Thanks,
Edwin.
2015-03-20 15:26 GMT+00:00 Carlos Simmerling <carlos.simmerling.gmail.com>:
> Yes check that, because it's easier to debug a test case failing than your
> specific inputs.
> Sorry Carlos for the incomplete information.
>
> Actually I didn't set any born radii in leap, I didn't know about it but
> now I do --thanks. So, because I didn't set any born radii, it should
> have used the default (PBRadii set to mbondi), which according to the
> manual is the recommended value when using igb=1, which I am using.
>
> I don't know about the test because it is run on a cluster but I really
> think so because the administrators are very careful. I am at the
> University of Birmingham, UK. I will see if I can get that information.
>
> Thanks,
> Edwin.
>
> On Thu, 2015-03-19 at 18:26 -0400, Carlos Simmerling wrote:
> > Thanks, but I also asked which radii set you used in leap. Also, did it
> > pass the tests? Until we know those we can't help.
> > On Mar 19, 2015 6:05 PM, "Edwin Helbert Aponte Angarita" <
> > helbert2a.gmail.com> wrote:
> >
> > > I am using the The Hawkins, Cramer, Truhlar model (igb=1). I am using
> > > rgbmax=999. and cut=999.
> > >
> > > Thanks,
> > > Edwin.
> > >
> > > On Thu, 2015-03-19 at 16:35 -0400, Carlos Simmerling wrote:
> > > > did your installation pass the test cases?
> > > > also, the GB model and radii set may be more relevant than the force
> > > field,
> > > > which are you using?
> > > >
> > > > On Thu, Mar 19, 2015 at 4:21 PM, Edwin Helbert Aponte Angarita <
> > > > helbert2a.gmail.com> wrote:
> > > >
> > > > > Hi, I think it is worth pointing out that I am using ff99SB.
> > > > >
> > > > > Thanks.
> > > > >
> > > > > On Thu, 2015-03-19 at 19:30 +0000, Edwin Helbert Aponte Angarita
> wrote:
> > > > > > Hello, thank you for your replies.
> > > > > >
> > > > > >
> > > > > > I am using Amber 12.0 on a cluster running Scientific Linux 6.6
> > > > > > (kernel 2.6.32-504.3.3) and manages jobs using torque.
> > > > > >
> > > > > >
> > > > > > I got the following message when loading amber:
> > > > > >
> > > > > > module load apps/amber/v12.0
> > > > > > Amber and AmberTools v12.0 serial and parallel
> > > > > > OpenMPI v1.6.3 for Intel 2013.0.079 with torque and infiniband
> > > support
> > > > > > Intel compilers v2013.0.079
> > > > > >
> > > > > >
> > > > > > I haven't found update_amber anywhere, maybe the administrator
> > > deleted
> > > > > > it. I looked for it using:
> > > > > > find /gpfs/apps/amber/amber12.0/ -iname \*update\*
> > > > > >
> > > > > >
> > > > > > Is there any other way I can check the patches applied?
> > > > > >
> > > > > >
> > > > > > I am getting an ERROR IN SETPAR() in the .out file:
> > > > > >
> > > > > > &cntrl
> > > > > >
> > > > > > imin=1,
> > > > > >
> > > > > > maxcyc=2000,
> > > > > >
> > > > > > ncyc=1000,
> > > > > >
> > > > > > cut=999.,
> > > > > >
> > > > > > rgbmax=999.,
> > > > > >
> > > > > > igb=1,
> > > > > >
> > > > > > ntb=0,
> > > > > >
> > > > > > ntpr=50,
> > > > > >
> > > > > > ntwx=50,
> > > > > >
> > > > > > ioutfm=1,
> > > > > > /
> > > > > >
> > > > > >
> > > > >
> > >
>
> --------------------------------------------------------------------------------
> > > > > > 1. RESOURCE USE:
> > > > > >
> > > > >
> > >
>
> --------------------------------------------------------------------------------
> > > > > >
> > > > > > | Flags:
> > > > > > MPI
> > > > > > | New format PARM file being parsed.
> > > > > > | Version = 1.000 Date = 03/17/15 Time = 17:22:13
> > > > > > NATOM = 352 NTYPES = 8 NBONH = 178 MBONA =
> 173
> > > > > > NTHETH = 397 MTHETA = 236 NPHIH = 718 MPHIA =
> 679
> > > > > > NHPARM = 0 NPARM = 0 NNB = 1863 NRES =
> 34
> > > > > > NBONA = 173 NTHETA = 236 NPHIA = 679 NUMBND =
> 12
> > > > > > NUMANG = 25 NPTRA = 24 NATYP = 10 NPHB =
> 0
> > > > > > IFBOX = 0 NMXRS = 23 IFCAP = 0 NEXTRA =
> 0
> > > > > > NCOPY = 0
> > > > > >
> > > > > > Implicit solvent radii are modified Bondi radii
> > > > > > (mbondi)
> > > > > >
> > > > > > | Memory Use Allocated
> > > > > > | Real 25582
> > > > > > | Hollerith 1092
> > > > > > | Integer 38655
> > > > > > | Max Pairs 1
> > > > > > | nblistReal 0
> > > > > > | nblist Int 0
> > > > > > | Total 355 kbytes
> > > > > >
> > > > > > | Note: 1-4 EEL scale factors were NOT found in the topology
> file.
> > > > > > | Using default value of 1.2.
> > > > > >
> > > > > > | Note: 1-4 VDW scale factors were NOT found in the topology
> file.
> > > > > > | Using default value of 2.0.
> > > > > > | Duplicated 0 dihedrals
> > > > > > | Duplicated 0 dihedrals
> > > > > >
> > > > > >
> > > > >
> > >
>
> --------------------------------------------------------------------------------
> > > > > > 2. CONTROL DATA FOR THE RUN
> > > > > >
> > > > >
> > >
>
> --------------------------------------------------------------------------------
> > > > > >
> > > > > > ACE
> > > > > >
> > > > > > General flags:
> > > > > > imin = 1, nmropt = 0
> > > > > >
> > > > > > Nature and format of input:
> > > > > > ntx = 1, irest = 0, ntrx = 1
> > > > > >
> > > > > > Nature and format of output:
> > > > > > ntxo = 1, ntpr = 50, ntrx = 1,
> ntwr
> > > > > > = 500
> > > > > > iwrap = 0, ntwx = 50, ntwv = 0,
> ntwe
> > > > > > = 0
> > > > > > ioutfm = 1, ntwprt = 0, idecomp = 0,
> > > > > > rbornstat= 0
> > > > > >
> > > > > > Potential function:
> > > > > > ntf = 1, ntb = 0, igb = 1,
> nsnb
> > > > > > = 25
> > > > > > ipol = 0, gbsa = 0, iesp = 0
> > > > > > dielc = 1.00000, cut = 999.00000, intdiel =
> 1.00000
> > > > > > saltcon = 0.00000, offset = 0.09000, gbalpha=
> 1.00000
> > > > > > gbbeta = 0.00000, gbgamma = 0.00000, surften =
> 0.00500
> > > > > > rdt = 0.00000, rgbmax = 999.00000 extdiel =
> 78.50000
> > > > > > alpb = 0
> > > > > >
> > > > > > Frozen or restrained atoms:
> > > > > > ibelly = 0, ntr = 0
> > > > > >
> > > > > > Energy minimization:
> > > > > > maxcyc = 2000, ncyc = 1000, ntmin = 1
> > > > > > dx0 = 0.01000, drms = 0.00010
> > > > > >
> > > > > > | MPI Timing options:
> > > > > > | profile_mpi = 0
> > > > > > | INFO: Old style inpcrd file read
> > > > > >
> > > > > >
> > > > > >
> > > > >
> > >
>
> --------------------------------------------------------------------------------
> > > > > > 3. ATOMIC COORDINATES AND VELOCITIES
> > > > > >
> > > > >
> > >
>
> --------------------------------------------------------------------------------
> > > > > >
> > > > > > ACE
> > > > > > begin time read from input coords = 0.000 ps
> > > > > >
> > > > > > Number of triangulated 3-point waters found: 0
> > > > > > ERROR IN SETPAR() upon atom distribution
> > > > > >
> > > > > > -------------------------------------------------
> > > > > >
> > > > > >
> > > > > > However, if I run the same minimize the same system with the
> > > > > > following .in file everything works:
> > > > > >
> > > > > >
> > > > > >
> > > > > > &cntrl
> > > > > >
> > > > > > imin=1,
> > > > > >
> > > > > > maxcyc=200,
> > > > > >
> > > > > > ncyc=100,
> > > > > >
> > > > > > cut=999.,
> > > > > >
> > > > > > rgbmax=999.,
> > > > > >
> > > > > > igb=1,
> > > > > >
> > > > > > ntb=0,
> > > > > >
> > > > > > ntpr=5,
> > > > > >
> > > > > > ntwx=5,
> > > > > >
> > > > > > ioutfm=1,
> > > > > > /
> > > > > >
> > > > > >
> > > > > > Thanks,
> > > > > >
> > > > > >
> > > > > > Edwin.
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > > 2015-03-19 2:50 GMT+00:00 Daniel Roe <daniel.r.roe.gmail.com>:
> > > > > > Hi,
> > > > > >
> > > > > > On Wed, Mar 18, 2015 at 10:41 AM, Edwin Helbert Aponte
> > > > > > Angarita
> > > > > > <helbert2a.gmail.com> wrote:
> > > > > > > and I get a very nice plot showing how the peptide
> > > converges
> > > > > > to a local
> > > > > > > minimum and does not change noticeable any more.
> However, I
> > > > > > cannot get
> > > > > > > sander nor sander.MPI to write the trajectory file if I
> use
> > > > > > generalized
> > > > > > > Born implicit solvent. In that case I use:
> > > > > >
> > > > > > Do you get any output at all (i.e. in your mdout or
> mdinfo
> > > > > > files)? Are
> > > > > > your GB simulations completing without error?
> > > > > >
> > > > > > -Dan
> > > > > >
> > > > > > >
> > > > > > > &cntrl
> > > > > > > imin=1,
> > > > > > > maxcyc=2000,
> > > > > > > ncyc=1000,
> > > > > > > cut=999.,
> > > > > > > rgbmax=999.,
> > > > > > > igb=1,
> > > > > > > ntb=0,
> > > > > > > ntpr=50,
> > > > > > > ntwx=50,
> > > > > > > ioutfm=1,
> > > > > > > /
> > > > > > >
> > > > > > > and I am setting approppriatelly -i -o -p -c -r -x.
> > > > > > >
> > > > > > > Do you know how can I get the trajectory when using
> > > > > > generalized Born
> > > > > > > implicit solvent? I only found a very old similar post
> (
> > > > > > > http://archive.ambermd.org/200502/0076.html) but is
> not
> > > > > > really helpful.
> > > > > > >
> > > > > > > Thanks,
> > > > > > >
> > > > > > > Edwin.
> > > > > > > _______________________________________________
> > > > > > > AMBER mailing list
> > > > > > > AMBER.ambermd.org
> > > > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > > >
> > > > > >
> > > > > >
> > > > > > --
> > > > > > -------------------------
> > > > > > Daniel R. Roe, PhD
> > > > > > Department of Medicinal Chemistry
> > > > > > University of Utah
> > > > > > 30 South 2000 East, Room 307
> > > > > > Salt Lake City, UT 84112-5820
> > > > > > http://home.chpc.utah.edu/~cheatham/
> > > > > > (801) 587-9652
> > > > > > (801) 585-6208 (Fax)
> > > > > >
> > > > > > _______________________________________________
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> > > > > >
> > > > > >
> > > > >
> > > > >
> > > > >
> > > > > _______________________________________________
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Received on Fri Mar 20 2015 - 12:30:02 PDT
