[gmx-users] LINCS warning

2014-04-27 Thread Gaurav Saraf IDD M Tech Biochem. Engg, IIT (BHU) 
Dear Gromacs user,

After I give the command for nvt, I get the following error:
starting mdrun 'Protein in water'
15 steps,300.0 ps.

Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.410417, max 7.601056 (between atoms 188 and 192)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
177179   40.70.1342   0.2195  0.1330
179181   69.60.1484   0.2977  0.1470
179180   51.10.1005   0.1744  0.1000
181195   75.80.1543   0.2575  0.1530
181182   77.00.1549   0.6596  0.1530
182183   47.80.1549   0.3570  0.1530
183186   76.80.1407   1.1049  0.1390
183184   76.10.1406   0.9974  0.1390
186187   69.80.1097   0.3696  0.1090
188192   79.10.1403   1.1955  0.1390
188189   72.00.1099   0.3759  0.1090
190192   77.90.1404   1.1212  0.1390
190191   71.50.1099   0.3818  0.1090
195197   34.80.1345   0.1997  0.1330
195196   39.90.1237   0.1807  0.1230
   4571   4569   40.00.1404   0.0953  0.1400
   4570   4569   91.20.1245   0.1846  0.1230
   4572   4571   31.30.1005   0.1253  0.1000
184188   41.10.1397   0.2396  0.1390
184185   72.10.1097   0.4012  0.1090
193194   82.90.1015   0.6012  0.1000
Wrote pdb files with previous and current coordinates
step 0
Step 1, time 0.002 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 2524.656192, max 85802.020979 (between atoms 170 and 177)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
170177   81.90.1793 13127.8622  0.1530
177179   94.90.2195 12873.2695  0.1330
179181   88.60.2977 4411.0838  0.1470
181195   96.60.2575 963.1998  0.1530
195197   87.40.1997 250.2422  0.1330
195196   80.60.1807 246.3256  0.1230
181182   83.50.6596 33817.6412  0.1530
182183   90.90.3570 1629245.5886  0.1530
179180  150.70.1744 806.4780  0.1000
177178   86.50.1487 13025.8466  0.1230
170171  123.70.1636 1099.0521  0.1530
172174  112.90.1334 124.2084  0.1330
172173  119.80.1234 122.9154  0.1230
174176   41.30.1000  19.2568  0.1000
141149   30.50.1530   0.1924  0.1530
149151  125.20.1330  18.9674  0.1330
149150   34.10.1230   0.1614  0.1230
151153   35.80.1471  28.7745  0.1470
151152   83.30.1000  18.9746  0.1000
166167  115.50.1238 341.2685  0.1230
153166  117.80.1538 365.5008  0.1530
153154   37.00.1531  14.8979  0.1530
154155   90.80.1530  15.6791  0.1530
155158   33.40.1390   0.1782  0.1390
155156   32.80.1390   0.1771  0.1390
168170  141.40.1596 1274.6369  0.1470
168169   93.70.1015 232.5375  0.1000

Step 1, time 0.002 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 12958124.333813, max 292691795.227618 (between atoms 184 and 188)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
203204   32.10.1470   0.1744  0.1470
201202   74.00.1532   1.1957  0.1530
202203  117.70.1530   0.3991  0.1530
208210   59.20.1359   3.5580  0.1330
208209   73.20.1256   1.9933  0.1230
210212   74.80.1480   1.9178  0.1470
210211   93.80.1007   1.5815  0.1000
177179   94.90.2195 12873.2691  0.1330
177178   86.50.1487 13025.8467  0.1230
170177   81.90.1793 13127.8623  0.1530
170171  123.70.1636 1099.0521  0.1530
172174  112.90.1334 124.2084  0.1330
174176   41.30.1000  19.2568  0.1000
172173  119.80.1234 122.9154  0.1230
168170  141.40.1596 1274.6369  0.1470
168169   93.70.1015 232.5375  0.1000
166167  115.50.1238 341.2681  0.1230
153166  117.80.1538 365.5039  0.1530
153154   37.00.1531  14.8978  0.1530
151153   35.80.1471  28.7776  0.1470
179181   88.60.2977 4411.0814  0.1470
179180  150.70.1744 806.4798  0.1000
212217  118.10.1531   1.2961  0.1530
212213  109.40.1531   1.3254  0.1530
213214   39.00.1530   0.2085  0.1530
155156   32.80.1390   0.1771  0.1390
155158   33.40.1390   0.1782  0.1390
154155   90.80.1530  15.6794  0.1530
151

[gmx-users] Help regarding potential energy

2014-04-26 Thread Gaurav Saraf IDD M Tech Biochem. Engg, IIT (BHU) 
Dear Gromacs users,
I am doing a protein-peptide simulation using gromos43a1 forcefield
(as per the tutorial)
When i do the energy minimization step before beginning equilibration,
I get the following results:

Steepest Descents converged to Fmax  1000 in 652 steps
Potential Energy  = -8.04234816499126e+05
Maximum force =  9.71976935137859e+02 on atom 4612
Norm of force =  2.70955252439520e+01

But when I check with g_energy_d -f em.edr (and then 10 0 {for
potential}), I get

Energy  Average   Err.Est.   RMSD  Tot-Drift
---
Potential1.36118e+091.3e+09 1.52478e+10
-7.91307e+09  (kJ/mol)

The potential is showing positive... what could be wrong?

Thanking you,
Regards,
Gaurav.
School of Biochemical engineering
IIT BHU, INDIA.
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[gmx-users] help regarding building topology of Lanitibiotics (small natural peptides)

2014-03-28 Thread Gaurav Saraf IDD M Tech Biochem. Engg, IIT (BHU) 
Respected Sir/Ma'am

I am new to the field of simulations and want to perform
protein-peptide simulations. I am facing troubles with building the
topology for my peptides as they contain various modified amino acids
which the rtp does not recognise.

Attachments: one of the pdb file of a lantibiotic (2KTO is the RCSB code)

Thanking you,


Yours sincerely,
Gaurav
School of Biochemical Engineering.
Indian Insitute of Technology (BHU), Varanasi.
India.
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