[gmx-users] About Em and Equlibration With Lincs Algorithim
Justin Lemkul
jalemkul at vt.edu
Tue Oct 9 20:09:53 CEST 2012
On 10/9/12 12:38 PM, vidhya sankar wrote:
> Dear Justin Than you for your previous Reply
>
> I am doing EM for My cyclic peptide using following EM. MDP
>
> ; ions.mdp - used as input into grompp to generate ions.tpr
> ; Parameters describing what to do, when to stop and what to save
> integrator = steep ; Algorithm (steep = steepest descent minimization)
> emtol = 1000 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm
> emstep = 0.01 ; Energy step size
> nsteps = 50000 ; Maximum number of (minimization) steps to perform
> constraints = none
> ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions
> nstlist = 1 ; Frequency to update the neighbor list and long range forces
> ns_type = grid ; Method to determine neighbor list (simple, grid)
> rlist = 1.4 ; Cut-off for making neighbor list (short range forces)
> coulombtype = PME ; Treatment of long range electrostatic interactions
> rcoulomb = 1.4 ; Short-range electrostatic cut-off
> rvdw = 1.4 ; Short-range Van der Waals cut-off
> pbc = xyz ; Periodic Boundary Conditions
>
> Steepest Descents converged to machine precision in 2885 steps,
> but did not reach the requested Fmax < 1000.
> Potential Energy = -2.88282144376129e+05
> Maximum force = 1.25808872222753e+03 on atom 107
> Norm of force = 4.38175991068554e+01
>
> i Have done Five time EM using emtol = 1000
>
> Every Attempt became failed Then i planned to use emtol = 1500
>
> In Previus Mail You Quoted the Possible emtol = 1000 For Most of Protein in Water But in My case it is not so Because the ring is so stained
>
> So I use emtol = 1500 it is converged Successfully as follows
>
> writing lowest energy coordinates.
>
> Steepest Descents converged to Fmax < 1500 in 2868 steps
> Potential Energy = -2.88282144367798e+05
> Maximum force = 1.31510551954873e+03 on atom 107
> Norm of force = 4.39665399153860e+01
>
>
> If I continue further NPT equlibration with Lincs Algorithim it shows Error aS follows
>
> Step 0, time 0 (ps) LINCS WARNING
> relative constraint deviation after LINCS:
> rms 1167.301393, max 4514.205877 (between atoms 164 and 168)
> bonds that rotated more than 30 degrees:
> atom 1 atom 2 angle previous, current, constraint length
> 164 168 154.6 2.3463 690.8265 0.1530
> 164 168 154.6 2.3463 690.8265 0.1530
> 165 166 118.1 1.3451 224.6411 0.1530
> 165 166 118.1 1.3451 224.6411 0.1530
> 166 167 67.4 1.1731 86.2422 0.1530
> 166 167 67.4 1.1731 86.2422 0.1530
> 168 169 141.9 2.9836 281.9632 0.1230
> 168 169 141.9 2.9836 281.9632 0.1230
> 1 2 66.8 0.0735 2.3215 0.1000
> 1 168 59.8 2.7313 251.2519 0.1330
> 1 3 126.5 0.1241 2.3286 0.1470
> 156 157 96.0 0.1464 0.3827 0.1470
> 157 161 110.5 0.1604 0.4095 0.1530
> 157 158 95.9 0.1523 0.3563 0.1530
> 161 163 31.2 1.3955 148.8536 0.1330
> 161 162 81.6 0.1293 0.6410 0.1230
> 163 164 137.9 3.2852 517.7200 0.1470
> 163 164 137.9 3.2852 517.7200 0.1470
> 3 16 92.2 0.1534 2.8760 0.1530
> 3 4 93.9 0.1528 2.8694 0.1530
>
> Back Off! I just backed up step0b_n1.pdb to ./#step0b_n1.pdb.1#
>
> Back Off! I just backed up step0c_n1.pdb to ./#step0c_n1.pdb.1#
> Wrote pdb files with previous and current coordinates
> starting mdrun 'L-22 CYCLIC PEPTIDE'
> 100000 steps, 20.0 ps.
> Warning: 1-4 interaction between 166 and 168 at distance 2.841 which is larger than the 1-4 table size 2.400 nm
> These are ignored for the rest of the simulation
> This usually means your system is exploding,
> if not, you should increase table-extension in your mdp file
> or with user tables increase the table size
>
>
> step 0: Water molecule starting at atom 7007 can not be settled.
> Check for bad contacts and/or reduce the timestep if appropriate.
> 124 125 111.2 0.1530 297.2103 0.1530
> 125 127 38.3 0.1530 0.1981 0.1530
> 121 123 98.7 0.1470 1978.8023 0.1470
> 119 121 139.2 0.1330 222.7882 0.1330
> 119 120 35.3 0.1230 0.1629 0.1230
> 106 119 33.3 0.1530 0.1945 0.1530
>
> step 0: Water molecule starting at atom 6461 can not be settled.
> Check for bad contacts and/or reduce the timestep if appropriate.
>
> Back Off! I just backed up step0b_n1.pdb to ./#step0b_n1.pdb.2#
>
>
>
> step 0: Water molecule starting at atom 2855 can not be settled.
> Check for bad contacts and/or reduce the timestep if appropriate.
>
> Back Off! I just backed up step0c_n1.pdb to ./#step0c_n1.pdb.2#
> Wrote pdb files with previous and current coordinates
> Wrote pdb files with previous and current coordinates
> Wrote pdb files with previous and current coordinates
>
>
> How TO Rectify the above errror Even I I have Visualised the EM.gro file in VMD It seem to be good (it Indicates That topology is correct) Must I use Lincs Algorithim During NPT Equlibration If I Run Without LINCS It runs Sucessfully
>
>
You don't necessarily have to use LINCS, but constraints are commonly applied in
order to use longer timesteps, and rigid bonds are a better model of reality.
Simple visualization does not indicate that the topology is sound. The fact
that your EM is insufficient and that the equilibration run fails instantly
indicates that the starting geometry, topology, or both, are problematic. Based
on the available information, we can't tell what is the source of the problem.
Follow the diagnostic steps at
http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System
and report back with your findings.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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