The box was used for doing the MD simulations with two states with
different charges on the cofactor.
Now I'm estimating amber FF single point energies for one trajectory with
the parameters for the other state.
Thus I'm using input set for a nonperodic system. (Please suggest if this
is physically meaningful or not.)
These calculations ran smoothly for systems where MD was done with waterbox
size of 10, 15A but I'm getting this error with a box size of 30A.
Please also comment on how other sp calculations on MD trajectories are
usually set in amber with sander and pmemd.
Do you use the periodic system or a droplet in gas phase?
Thanks a lot for your help.
Best regards
On Sat, Feb 20, 2021, 18:18 Carlos Simmerling <carlos.simmerling.gmail.com>
wrote:
> it's a bit confusing, you talk about your box size but your inputs set a
> non-periodic system, meaning no box but just a droplet in the gas phase. is
> that really what you want to simulate?
> and with nearly 100,000 atoms and large cutoff, you will get many many
> atom pairs.
> Are you sure you don't want to do this in a periodic box using PME and a
> cutoff of around 10 angstroms on the pairlist?
>
>
> On Fri, Feb 19, 2021 at 11:07 PM Vaibhav Dixit <vaibhavadixit.gmail.com>
> wrote:
>
>> Dear All,
>> I ran MD with 10, 15 and 30A TIP3PBOX to understand the effect of box size
>> on relative FF energies between two systems.
>> The calculations when well with 10 and 15A box size.
>> But I'm getting the following error in mdout file with the system setup
>> with 30A TIP3PBOX.
>> I tried by reducing the cut values 9999, 999, 199 and 99 but got the same
>> error message. For the 30A system the box size is > 100 A and 32414
>> waters
>> (tleap output pasted below).
>> Can you please help me understand if this error is due to memory or some
>> other factor?
>> I can't find this variable in the manual and there is little info on the
>> archives about the same (http://archive.ambermd.org/201101/0159.html).
>> Please do let me know if additional information is needed about my system
>> setup.
>> Looking forward to valuable suggestions from the list.
>> thank you and best regards
>>
>> single point energy calculations of ferric state coordinates using ferrous
>> parameters
>> &cntrl
>>
>> ntx=1, ntpr=1, ntwx=1,
>>
>> imin=5, maxcyc=1, !Single-point energy calculation on each frame
>>
>> ntb=0, !Non-periodic
>>
>> cut=99., !Calculate all solute-solute interactions
>>
>> /
>>
>>
>>
>>
>>
>> --------------------------------------------------------------------------------
>> 1. RESOURCE USE:
>>
>> --------------------------------------------------------------------------------
>>
>> | Flags: MPI
>>
>> | NONPERIODIC ntb=0 and igb=0: Setting up nonperiodic simulation
>> |Largest sphere to fit in unit cell has radius = 78.915
>> | New format PARM file being parsed.
>> | Version = 1.000 Date = 02/19/21 Time = 21:23:34
>> NATOM = 99456 NTYPES = 19 NBONH = 98343 MBONA = 1148
>> NTHETH = 2507 MTHETA = 1581 NPHIH = 4977 MPHIA = 4857
>> NHPARM = 0 NPARM = 0 NNB = 141965 NRES = 32557
>> NBONA = 1148 NTHETA = 1581 NPHIA = 4857 NUMBND = 107
>> NUMANG = 252 NPTRA = 194 NATYP = 54 NPHB = 1
>> IFBOX = 1 NMXRS = 72 IFCAP = 0 NEXTRA = 0
>> NCOPY = 0
>>
>> | CMAP information read from topology file:
>> *Unreasonably large value for MAXPR: 0.49E+10*
>>
>> truncated tleap output
>> --------------------------
>>
>> Solute vdw bounding box: 37.769 41.632 46.477
>> Total bounding box for atom centers: 97.769 101.632 106.477
>> Solvent unit box: 18.774 18.774 18.774
>> Total vdw box size: *100.860 104.558 109.778*
>> angstroms.
>> Volume: 1157694.469 A^3
>> Total mass 599714.586 amu, Density 0.860 g/cc
>> Added *32414* residues.
>>
>> --
>>
>> Regards,
>>
>> Dr. Vaibhav A. Dixit,
>>
>> Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The
>> University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
>> AND
>> Assistant Professor,
>> Department of Pharmacy,
>> ▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄
>> Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
>> VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
>> India.
>> Phone No. +91 1596 255652, Mob. No. +91-7709129400,
>> Email: vaibhav.dixit.pilani.bits-pilani.ac.in, vaibhavadixit.gmail.com
>> http://www.bits-pilani.ac.in/pilani/vaibhavdixit/profile
>> https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
>>
>> ORCID ID: https://orcid.org/0000-0003-4015-2941
>>
>> http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
>>
>> P Please consider the environment before printing this e-mail
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Received on Sat Feb 20 2021 - 05:30:02 PST
