[gmx-users] g_current

[Nilesh Dhumal]

Here is full gmxcheck

Checking file water.trr
trn version: GMX_trn_file (single precision)
Reading frame       0 time    0.000
# Atoms  2592
Last frame        100 time   20.000


Item        #frames Timestep (ps)
Step           101    0.2
Time           101    0.2
Lambda         101    0.2
Coords         101    0.2
Velocities       0
Forces           0
Box            101    0.2
Checking coordinate file water.tpr
Reading file water.tpr, VERSION 4.5.5 (single precision)
Reading file water.tpr, VERSION 4.5.5 (single precision)
2592 atoms in file
coordinates found
box         found
velocities  found

Kinetic energy: 9695.08 (kJ/mol)
Assuming the number of degrees of freedom to be Natoms * 3 or Natoms * 2,
the velocities correspond to a temperature of the system
of 299.908 K or 449.862 K respectively.

Checking for atoms closer than 0.8 and not between 0.4 and 0.7,
relative to sum of Van der Waals distance:

WARNING: masses and atomic (Van der Waals) radii will be determined
         based on residue and atom names. These numbers can deviate
         from the correct mass and radius of the atom type.

no close atoms found

Atoms outside box ( 3.0273 3.0273 3.0273 ):
(These may occur often and are normally not a problem)
atom# name  residue r_vdw  coordinate
   25  HW1  SOL   9 0.04    2.15   1.22   3.06
   77  HW2  SOL  26 0.04    1.69   1.52   3.03
   80  HW2  SOL  27 0.04    1.29   2.18   3.03
   87   OW  SOL  30 0.105   2.99  0.646   3.03
   88  HW1  SOL  30 0.04    3.06  0.584   3.07
  100  HW1  SOL  34 0.04  -0.0643   1.88  0.849
  196  HW1  SOL  66 0.04     1.8   1.92 -0.0014
  219   OW  SOL  74 0.105   3.03   1.97   0.61
  221  HW2  SOL  74 0.04    3.08   2.05  0.649
  238  HW1  SOL  80 0.04    1.33   2.99 -0.0012
(maybe more)





>
>
> On 4/15/14, 2:18 PM, Nilesh Dhumal wrote:
>> I checked with gmx_check, its says velocities  found.
>>
>
> Please provide the full gmxcheck output.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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