[gmx-users] simulation problem whit lincs
Osmany Guirola Cruz
osmany.guirola at cigb.edu.cu
Tue Dec 30 21:46:01 CET 2003
NO .. It's a cluster of duals pentiums III
-----Original Message-----
From: Gerrit Groenhof [mailto:G.Groenhof at chem.rug.nl]
Sent: Tuesday, December 30, 2003 2:18 PM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] simulation problem whit lincs
Hi
Sorry I have no solution to your problem yet, but out of
curiosity, are you running on an AMD cpu?
Gerrit
>
> I am doing a simulation of system with one protein and a peptide i do
> all steps necesary for the simulation(minimization, genion ,position
> restrain etc...) when i run the final step(MD) runs whitout problem
> during some time.. these is the error Step 161731, time 323.462 (ps)
> LINCS WARNING relative constraint deviation after LINCS:
> max 598.181541 (between atoms 245 and 253) rms 30.851655
> bonds that rotated more than 30 degrees:
> atom 1 atom 2 angle previous, current, constraint length
> 228 230 71.1 0.1526 0.1637 0.1330
> 230 231 89.9 0.1254 0.1791 0.1000
> 230 232 93.9 0.1431 3.1038 0.1470
> 232 233 55.3 0.1637 3.4467 0.1530
> 232 241 166.2 0.5243 18.0264 0.1530
> 233 234 142.6 0.1816 0.5641 0.1530
> 234 235 63.4 0.1569 0.2542 0.1530
> 235 236 38.4 0.1531 0.2049 0.1530
> 241 242 167.2 0.7252 17.4063 0.1230
> 241 243 174.9 2.5790 33.7894 0.1330
> 243 244 174.5 2.9965 32.4020 0.1000
> 243 245 178.2 5.9836 63.5208 0.1470
> 245 246 169.7 6.5919 56.3915 0.1530
> 245 253 179.0 7.9640 91.6748 0.1530
> 246 247 168.4 2.6903 9.8748 0.1530
> 247 248 164.5 5.1313 20.9254 0.1530
> 248 249 172.3 6.8486 21.0018 0.1230
> 248 250 169.4 6.8948 21.9502 0.1330
> 250 251 116.6 1.2659 10.9623 0.1000
> 250 252 121.4 1.0057 11.1177 0.1000
> 253 254 174.8 4.7518 59.2405 0.1230
> 253 255 177.1 5.0970 68.2804 0.1330
> 255 256 169.2 1.4168 31.4833 0.1000
> 255 257 170.7 1.6224 32.8697 0.1470
> 257 258 161.4 0.3731 16.8051 0.1530
> 257 266 178.5 0.4607 21.1382 0.1530
> 258 259 141.7 0.2932 3.7214 0.1530
> 259 260 52.3 0.2080 0.7846 0.1530
> 260 261 62.1 0.1605 0.1708 0.1530
> 261 262 71.1 0.1480 0.1571 0.1470
> 262 263 47.3 0.1000 0.1444 0.1000
> 262 264 46.5 0.1000 0.1433 0.1000
> 262 265 43.5 0.0999 0.1388 0.1000
> 266 267 168.8 0.2212 9.2796 0.1230
> 266 268 168.9 0.2406 9.6550 0.1330
> 268 269 62.6 0.1641 2.0107 0.1000
> 268 270 41.4 0.2100 2.1612 0.1470
> 270 271 125.0 0.1688 0.1061 0.1530
> 271 272 41.6 0.1264 0.0824 0.1230
> 271 273 64.9 0.1359 0.1026 0.1330
> 273 274 34.5 0.1004 0.1255 0.1000
> Constraint error in algorithm Lincs at step 161731
>
> Step 161731 Warning: pressure scaling more than 1%, mu: 1.02208
> 1.02208 1.02208
> Grid: -2147483648 x -2147483648 x -2147483648 cells
>
>
>
>
>
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