[gmx-users] lipid itp problem

Mon Jul 7 13:08:30 CEST 2008

"Broken bonds" are probably a visualization artefact.  Did you try what 
I suggested about minimizing just DPPC?  Better yet, try minimizing one 
single DPPC molecule in vacuo to see if that succeeds, then move up to 
the bilayer, etc.

Also, increasing the table-extension is usually not going to solve 
anything.  If you're system is exploding, it's going to explode no 
matter what the table-extension is.

-Justin

serdar durdagi wrote:
>
> Dear all,
>
>  
>
> Sorry for the previous e-mail format. I am writing again the problem.
>
>  
>
> I am trying to simulate drug at the binding site of the receptor 
> surrounded by DPPC bilayer system. I have problem at the energy 
> minimisation step. Always, I am getting below error message:
>
>  
>
> Warning: 1-4 interaction between 3642 and 3647 at distance 1.325 which 
> is larger than the 1-4 table size 1.000 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
>
>  
>
> Step= 0, Dmax= 1.0e-02 nm, Epot= 7.16584e+15 Fmax= 5.29841e+18, atom= 
> 2662 Step= 1, Dmax= 1.0e-02 nm, Epot= 1.19114e+12 Fmax= 2.10320e+14, 
> atom= 3605 Step= 2, Dmax= 1.2e-02 nm, Epot= 1.39843e+10 Fmax= 
> 8.84756e+11, atom= 2662 Step= 3, Dmax= 1.4e-02 nm, Epot= 1.36040e+09 
> Fmax= 5.31692e+10, atom= 2661
>
>  
>
>  
>
> When I try to increase table-extension to more than 1.0, 1-4 
> interaction always increases.
>
>  
>
> I checked the *.gro file, it seems during the minimisation, bonds at 
> protein and drg molecules are fine however, bonds at the DPPC 
> molecules are broken.
>
>  
>
> I guess problem is at the *.itp file of dppc. I produced *.itp file of 
> DPPC from PRODRG. *itp file of lipid and *.mdp file for energy 
> minimisation are attached below. Could any body give a clue for the 
> solution? Many thanks in advanced.
>
>  
>
> Serdar Durdagi
>
>
>  
>
> ;
>
> ;
>
> ; This file was generated by PRODRG version 071121.0636
>
> ; PRODRG written/copyrighted by Daan van Aalten
>
> ; and Alexander Schuettelkopf
>
> ;
>
> ; Questions/comments to dava at davapc1.bioch.dundee.ac.uk
>
> ;
>
> ; When using this software in a publication, cite:
>
> ; A. W. Schuettelkopf and D. M. F. van Aalten (2004).
>
> ; PRODRG - a tool for high-throughput crystallography
>
> ; of protein-ligand complexes.
>
> ; Acta Crystallogr. D60, 1355--1363.
>
> ;
>
> ;
>
> [ moleculetype ]
>
> ; Name nrexcl
>
> MOL 3
>
> [ atoms ]
>
> ; nr type resnr resid atom cgnr charge mass
>
> 1 CH3 1 MOL C8 1 -0.033 15.0350
>
> 2 CH2 1 MOL C1 1 0.008 14.0270
>
> 3 CH2 1 MOL C45 1 0.008 14.0270
>
> 4 CH2 1 MOL C44 1 0.009 14.0270
>
> 5 CH2 1 MOL C43 1 0.008 14.0270
>
> 6 CH2 1 MOL C42 2 0.000 14.0270
>
> 7 CH2 1 MOL C41 2 0.000 14.0270
>
> 8 CH2 1 MOL C40 3 0.000 14.0270
>
> 9 CH2 1 MOL C39 3 0.000 14.0270
>
> 10 CH2 1 MOL C38 4 0.000 14.0270
>
> 11 CH2 1 MOL C37 4 0.000 14.0270
>
> 12 CH2 1 MOL C36 5 0.000 14.0270
>
> 13 CH2 1 MOL C35 5 0.000 14.0270
>
> 14 CH2 1 MOL C34 6 0.000 14.0270
>
> 15 CH2 1 MOL C33 7 0.036 14.0270
>
> 16 C 1 MOL C32 7 0.438 12.0110
>
> 17 O 1 MOL O46 7 -0.551 15.9994
>
> 18 OS 1 MOL O31 7 -0.160 15.9994
>
> 19 CS1 1 MOL C13 7 0.237 13.0190
>
> 20 CH2 1 MOL C12 8 0.000 14.0270
>
> 21 OS 1 MOL O11 9 -0.256 15.9994
>
> 22 P 1 MOL P8 9 0.998 30.9738
>
> 23 OM 1 MOL O10 9 -0.743 15.9994
>
> 24 OM 1 MOL O9 9 -0.743 15.9994
>
> 25 OS 1 MOL O4 9 -0.256 15.9994
>
> 26 CH2 1 MOL C3 10 0.041 14.0270
>
> 27 CH2 1 MOL C2 10 0.041 14.0270
>
> 28 NL 1 MOL N1 10 0.918 14.0067
>
> 29 CH3 1 MOL C6 11 0.000 15.0350
>
> 30 CH3 1 MOL C5 11 0.000 15.0350
>
> 31 CH3 1 MOL C7 12 0.000 15.0350
>
> 32 CS2 1 MOL C14 13 0.242 14.0270
>
> 33 OS 1 MOL O15 13 -0.162 15.9994
>
> 34 C 1 MOL C16 13 0.437 12.0110
>
> 35 O 1 MOL O30 13 -0.553 15.9994
>
> 36 CH2 1 MOL C17 13 0.036 14.0270
>
> 37 CH2 1 MOL C18 14 0.000 14.0270
>
> 38 CH2 1 MOL C19 14 0.000 14.0270
>
> 39 CH2 1 MOL C20 15 0.000 14.0270
>
> 40 CH2 1 MOL C21 15 0.000 14.0270
>
> 41 CH2 1 MOL C22 16 0.000 14.0270
>
> 42 CH2 1 MOL C23 16 0.000 14.0270
>
> 43 CH2 1 MOL C24 17 0.000 14.0270
>
> 44 CH2 1 MOL C25 17 0.000 14.0270
>
> 45 CH2 1 MOL C26 18 0.000 14.0270
>
> 46 CH2 1 MOL C27 19 0.008 14.0270
>
> 47 CH2 1 MOL C28 19 0.008 14.0270
>
> 48 CH2 1 MOL C29 19 0.008 14.0270
>
> 49 CH2 1 MOL C9 19 0.009 14.0270
>
> 50 CH3 1 MOL C10 19 -0.033 15.0350
>
> [ bonds ]
>
> ; ai aj fu c0, c1, ...
>
> 1 2 1 0.153 334720.0 0.153 334720.0 ; C8 C1
>
> 2 3 1 0.153 334720.0 0.153 334720.0 ; C1 C45
>
> 3 4 1 0.153 334720.0 0.153 334720.0 ; C45 C44
>
> 4 5 1 0.153 334720.0 0.153 334720.0 ; C44 C43
>
> 5 6 1 0.153 334720.0 0.153 334720.0 ; C43 C42
>
> 6 7 1 0.153 334720.0 0.153 334720.0 ; C42 C41
>
> 7 8 1 0.153 334720.0 0.153 334720.0 ; C41 C40
>
> 8 9 1 0.153 334720.0 0.153 334720.0 ; C40 C39
>
> 9 10 1 0.153 334720.0 0.153 334720.0 ; C39 C38
>
> 10 11 1 0.153 334720.0 0.153 334720.0 ; C38 C37
>
> 11 12 1 0.153 334720.0 0.153 334720.0 ; C37 C36
>
> 12 13 1 0.153 334720.0 0.153 334720.0 ; C36 C35
>
> 13 14 1 0.153 334720.0 0.153 334720.0 ; C35 C34
>
> 14 15 1 0.153 334720.0 0.153 334720.0 ; C34 C33
>
> 15 16 1 0.153 334720.0 0.153 334720.0 ; C33 C32
>
> 16 17 1 0.123 502080.0 0.123 502080.0 ; C32 O46
>
> 16 18 1 0.136 376560.0 0.136 376560.0 ; C32 O31
>
> 18 19 1 0.144 251040.0 0.144 251040.0 ; O31 C13
>
> 19 20 1 0.153 251040.0 0.153 251040.0 ; C13 C12
>
> 19 32 1 0.152 251040.0 0.152 251040.0 ; C13 C14
>
> 20 21 1 0.143 251040.0 0.143 251040.0 ; C12 O11
>
> 21 22 1 0.161 251040.0 0.161 251040.0 ; O11 P8
>
> 22 23 1 0.148 376560.0 0.148 376560.0 ; P8 O10
>
> 22 24 1 0.148 376560.0 0.148 376560.0 ; P8 O9
>
> 22 25 1 0.161 251040.0 0.161 251040.0 ; P8 O4
>
> 25 26 1 0.143 251040.0 0.143 251040.0 ; O4 C3
>
> 26 27 1 0.153 334720.0 0.153 334720.0 ; C3 C2
>
> 27 28 1 0.147 376560.0 0.147 376560.0 ; C2 N1
>
> 28 29 1 0.147 376560.0 0.147 376560.0 ; N1 C6
>
> 28 30 1 0.147 376560.0 0.147 376560.0 ; N1 C5
>
> 28 31 1 0.147 376560.0 0.147 376560.0 ; N1 C7
>
> 32 33 1 0.144 251040.0 0.144 251040.0 ; C14 O15
>
> 33 34 1 0.136 376560.0 0.136 376560.0 ; O15 C16
>
> 34 35 1 0.123 502080.0 0.123 502080.0 ; C16 O30
>
> 34 36 1 0.153 334720.0 0.153 334720.0 ; C16 C17
>
> 36 37 1 0.153 334720.0 0.153 334720.0 ; C17 C18
>
> 37 38 1 0.153 334720.0 0.153 334720.0 ; C18 C19
>
> 38 39 1 0.153 334720.0 0.153 334720.0 ; C19 C20
>
> 39 40 1 0.153 334720.0 0.153 334720.0 ; C20 C21
>
> 40 41 1 0.153 334720.0 0.153 334720.0 ; C21 C22
>
> 41 42 1 0.153 334720.0 0.153 334720.0 ; C22 C23
>
> 42 43 1 0.153 334720.0 0.153 334720.0 ; C23 C24
>
> 43 44 1 0.153 334720.0 0.153 334720.0 ; C24 C25
>
> 44 45 1 0.153 334720.0 0.153 334720.0 ; C25 C26
>
> 45 46 1 0.153 334720.0 0.153 334720.0 ; C26 C27
>
> 46 47 1 0.153 334720.0 0.153 334720.0 ; C27 C28
>
> 47 48 1 0.153 334720.0 0.153 334720.0 ; C28 C29
>
> 48 49 1 0.153 334720.0 0.153 334720.0 ; C29 C9
>
> 49 50 1 0.153 334720.0 0.153 334720.0 ; C9 C10
>
> [ pairs ]
>
> ; ai aj fu c0, c1, ...
>
> 1 4 1 ; C8 C44
>
> 2 5 1 ; C1 C43
>
> 3 6 1 ; C45 C42
>
> 4 7 1 ; C44 C41
>
> 5 8 1 ; C43 C40
>
> 6 9 1 ; C42 C39
>
> 7 10 1 ; C41 C38
>
> 8 11 1 ; C40 C37
>
> 9 12 1 ; C39 C36
>
> 10 13 1 ; C38 C35
>
> 11 14 1 ; C37 C34
>
> 12 15 1 ; C36 C33
>
> 13 16 1 ; C35 C32
>
> 14 17 1 ; C34 O46
>
> 14 18 1 ; C34 O31
>
> 15 19 1 ; C33 C13
>
> 16 20 1 ; C32 C12
>
> 16 32 1 ; C32 C14
>
> 17 19 1 ; O46 C13
>
> 18 21 1 ; O31 O11
>
> 18 33 1 ; O31 O15
>
> 19 22 1 ; C13 P8
>
> 19 34 1 ; C13 C16
>
> 20 23 1 ; C12 O10
>
> 20 24 1 ; C12 O9
>
> 20 25 1 ; C12 O4
>
> 20 33 1 ; C12 O15
>
> 21 26 1 ; O11 C3
>
> 21 32 1 ; O11 C14
>
> 22 27 1 ; P8 C2
>
> 23 26 1 ; O10 C3
>
> 24 26 1 ; O9 C3
>
> 25 28 1 ; O4 N1
>
> 26 29 1 ; C3 C6
>
> 26 30 1 ; C3 C5
>
> 26 31 1 ; C3 C7
>
> 32 35 1 ; C14 O30
>
> 32 36 1 ; C14 C17
>
> 33 37 1 ; O15 C18
>
> 34 38 1 ; C16 C19
>
> 35 37 1 ; O30 C18
>
> 36 39 1 ; C17 C20
>
> 37 40 1 ; C18 C21
>
> 38 41 1 ; C19 C22
>
> 39 42 1 ; C20 C23
>
> 40 43 1 ; C21 C24
>
> 41 44 1 ; C22 C25
>
> 42 45 1 ; C23 C26
>
> 43 46 1 ; C24 C27
>
> 44 47 1 ; C25 C28
>
> 45 48 1 ; C26 C29
>
> 46 49 1 ; C27 C9
>
> 47 50 1 ; C28 C10
>
> [ angles ]
>
> ; ai aj ak fu c0, c1, ...
>
> 1 2 3 1 111.0 460.2 111.0 460.2 ; C8 C1 C45
>
> 2 3 4 1 111.0 460.2 111.0 460.2 ; C1 C45 C44
>
> 3 4 5 1 111.0 460.2 111.0 460.2 ; C45 C44 C43
>
> 4 5 6 1 111.0 460.2 111.0 460.2 ; C44 C43 C42
>
> 5 6 7 1 111.0 460.2 111.0 460.2 ; C43 C42 C41
>
> 6 7 8 1 111.0 460.2 111.0 460.2 ; C42 C41 C40
>
> 7 8 9 1 111.0 460.2 111.0 460.2 ; C41 C40 C39
>
> 8 9 10 1 111.0 460.2 111.0 460.2 ; C40 C39 C38
>
> 9 10 11 1 111.0 460.2 111.0 460.2 ; C39 C38 C37
>
> 10 11 12 1 111.0 460.2 111.0 460.2 ; C38 C37 C36
>
> 11 12 13 1 111.0 460.2 111.0 460.2 ; C37 C36 C35
>
> 12 13 14 1 111.0 460.2 111.0 460.2 ; C36 C35 C34
>
> 13 14 15 1 111.0 460.2 111.0 460.2 ; C35 C34 C33
>
> 14 15 16 1 111.0 460.2 111.0 460.2 ; C34 C33 C32
>
> 15 16 17 1 121.0 502.1 121.0 502.1 ; C33 C32 O46
>
> 15 16 18 1 120.0 418.4 120.0 418.4 ; C33 C32 O31
>
> 17 16 18 1 120.0 418.4 120.0 418.4 ; O46 C32 O31
>
> 16 18 19 1 109.5 334.7 109.5 334.7 ; C32 O31 C13
>
> 18 19 20 1 109.5 284.5 109.5 284.5 ; O31 C13 C12
>
> 18 19 32 1 109.5 284.5 109.5 284.5 ; O31 C13 C14
>
> 20 19 32 1 109.5 251.0 109.5 251.0 ; C12 C13 C14
>
> 19 20 21 1 111.0 460.2 111.0 460.2 ; C13 C12 O11
>
> 20 21 22 1 120.0 397.5 120.0 397.5 ; C12 O11 P8
>
> 21 22 23 1 109.6 397.5 109.6 397.5 ; O11 P8 O10
>
> 21 22 24 1 109.6 397.5 109.6 397.5 ; O11 P8 O9
>
> 21 22 25 1 103.0 397.5 103.0 397.5 ; O11 P8 O4
>
> 23 22 24 1 120.0 585.8 120.0 585.8 ; O10 P8 O9
>
> 23 22 25 1 109.6 397.5 109.6 397.5 ; O10 P8 O4
>
> 24 22 25 1 109.6 397.5 109.6 397.5 ; O9 P8 O4
>
> 22 25 26 1 120.0 397.5 120.0 397.5 ; P8 O4 C3
>
> 25 26 27 1 109.5 460.2 109.5 460.2 ; O4 C3 C2
>
> 26 27 28 1 109.5 460.2 109.5 460.2 ; C3 C2 N1
>
> 27 28 29 1 109.5 376.6 109.5 376.6 ; C2 N1 C6
>
> 27 28 30 1 109.5 376.6 109.5 376.6 ; C2 N1 C5
>
> 27 28 31 1 109.5 376.6 109.5 376.6 ; C2 N1 C7
>
> 29 28 30 1 109.5 376.6 109.5 376.6 ; C6 N1 C5
>
> 29 28 31 1 109.5 376.6 109.5 376.6 ; C6 N1 C7
>
> 30 28 31 1 109.5 376.6 109.5 376.6 ; C5 N1 C7
>
> 19 32 33 1 109.5 284.5 109.5 284.5 ; C13 C14 O15
>
> 32 33 34 1 109.5 334.7 109.5 334.7 ; C14 O15 C16
>
> 33 34 35 1 120.0 418.4 120.0 418.4 ; O15 C16 O30
>
> 33 34 36 1 120.0 418.4 120.0 418.4 ; O15 C16 C17
>
> 35 34 36 1 121.0 502.1 121.0 502.1 ; O30 C16 C17
>
> 34 36 37 1 111.0 460.2 111.0 460.2 ; C16 C17 C18
>
> 36 37 38 1 111.0 460.2 111.0 460.2 ; C17 C18 C19
>
> 37 38 39 1 111.0 460.2 111.0 460.2 ; C18 C19 C20
>
> 38 39 40 1 111.0 460.2 111.0 460.2 ; C19 C20 C21
>
> 39 40 41 1 111.0 460.2 111.0 460.2 ; C20 C21 C22
>
> 40 41 42 1 111.0 460.2 111.0 460.2 ; C21 C22 C23
>
> 41 42 43 1 111.0 460.2 111.0 460.2 ; C22 C23 C24
>
> 42 43 44 1 111.0 460.2 111.0 460.2 ; C23 C24 C25
>
> 43 44 45 1 111.0 460.2 111.0 460.2 ; C24 C25 C26
>
> 44 45 46 1 111.0 460.2 111.0 460.2 ; C25 C26 C27
>
> 45 46 47 1 111.0 460.2 111.0 460.2 ; C26 C27 C28
>
> 46 47 48 1 111.0 460.2 111.0 460.2 ; C27 C28 C29
>
> 47 48 49 1 111.0 460.2 111.0 460.2 ; C28 C29 C9
>
> 48 49 50 1 111.0 460.2 111.0 460.2 ; C29 C9 C10
>
> [ dihedrals ]
>
> ; ai aj ak al fu c0, c1, m, ...
>
> 16 15 18 17 2 0.0 1673.6 0.0 1673.6 ; imp C32 C33 O31 O46
>
> 34 33 36 35 2 0.0 1673.6 0.0 1673.6 ; imp C16 O15 C17 O30
>
> 19 18 32 20 2 35.3 836.8 35.3 836.8 ; imp C13 O31 C14 C12
>
> 22 21 24 23 2 35.3 836.8 35.3 836.8 ; imp P8 O11 O9 O10
>
> 28 27 29 30 2 35.3 836.8 35.3 836.8 ; imp N1 C2 C6 C5
>
> 4 3 2 1 1 0.0 5.9 3 0.0 5.9 3 ; dih C44 C45 C1 C8
>
> 5 4 3 2 1 0.0 5.9 3 0.0 5.9 3 ; dih C43 C44 C45 C1
>
> 6 5 4 3 1 0.0 5.9 3 0.0 5.9 3 ; dih C42 C43 C44 C45
>
> 7 6 5 4 1 0.0 5.9 3 0.0 5.9 3 ; dih C41 C42 C43 C44
>
> 8 7 6 5 1 0.0 5.9 3 0.0 5.9 3 ; dih C40 C41 C42 C43
>
> 9 8 7 6 1 0.0 5.9 3 0.0 5.9 3 ; dih C39 C40 C41 C42
>
> 10 9 8 7 1 0.0 5.9 3 0.0 5.9 3 ; dih C38 C39 C40 C41
>
> 11 10 9 8 1 0.0 5.9 3 0.0 5.9 3 ; dih C37 C38 C39 C40
>
> 12 11 10 9 1 0.0 5.9 3 0.0 5.9 3 ; dih C36 C37 C38 C39
>
> 13 12 11 10 1 0.0 5.9 3 0.0 5.9 3 ; dih C35 C36 C37 C38
>
> 14 13 12 11 1 0.0 5.9 3 0.0 5.9 3 ; dih C34 C35 C36 C37
>
> 15 14 13 12 1 0.0 5.9 3 0.0 5.9 3 ; dih C33 C34 C35 C36
>
> 16 15 14 13 1 0.0 5.9 3 0.0 5.9 3 ; dih C32 C33 C34 C35
>
> 14 15 16 18 1 0.0 0.4 6 0.0 0.4 6 ; dih C34 C33 C32 O31
>
> 15 16 18 19 1 180.0 16.7 2 180.0 16.7 2 ; dih C33 C32 O31 C13
>
> 32 19 18 16 1 0.0 3.8 3 0.0 3.8 3 ; dih C14 C13 O31 C32
>
> 18 19 20 21 1 0.0 5.9 3 0.0 5.9 3 ; dih O31 C13 C12 O11
>
> 33 32 19 18 1 0.0 5.9 3 0.0 5.9 3 ; dih O15 C14 C13 O31
>
> 22 21 20 19 1 0.0 3.8 3 0.0 3.8 3 ; dih P8 O11 C12 C13
>
> 20 21 22 25 1 0.0 1.0 3 0.0 1.0 3 ; dih C12 O11 P8 O4
>
> 20 21 22 25 1 0.0 3.1 2 0.0 3.1 2 ; dih C12 O11 P8 O4
>
> 26 25 22 21 1 0.0 1.0 3 0.0 1.0 3 ; dih C3 O4 P8 O11
>
> 26 25 22 21 1 0.0 3.1 2 0.0 3.1 2 ; dih C3 O4 P8 O11
>
> 22 25 26 27 1 0.0 3.8 3 0.0 3.8 3 ; dih P8 O4 C3 C2
>
> 28 27 26 25 1 0.0 5.9 3 0.0 5.9 3 ; dih N1 C2 C3 O4
>
> 26 27 28 31 1 0.0 3.8 3 0.0 3.8 3 ; dih C3 C2 N1 C7
>
> 19 32 33 34 1 0.0 3.8 3 0.0 3.8 3 ; dih C13 C14 O15 C16
>
> 32 33 34 36 1 180.0 16.7 2 180.0 16.7 2 ; dih C14 O15 C16 C17
>
> 37 36 34 33 1 0.0 0.4 6 0.0 0.4 6 ; dih C18 C17 C16 O15
>
> 38 37 36 34 1 0.0 5.9 3 0.0 5.9 3 ; dih C19 C18 C17 C16
>
> 39 38 37 36 1 0.0 5.9 3 0.0 5.9 3 ; dih C20 C19 C18 C17
>
> 40 39 38 37 1 0.0 5.9 3 0.0 5.9 3 ; dih C21 C20 C19 C18
>
> 41 40 39 38 1 0.0 5.9 3 0.0 5.9 3 ; dih C22 C21 C20 C19
>
> 42 41 40 39 1 0.0 5.9 3 0.0 5.9 3 ; dih C23 C22 C21 C20
>
> 43 42 41 40 1 0.0 5.9 3 0.0 5.9 3 ; dih C24 C23 C22 C21
>
> 44 43 42 41 1 0.0 5.9 3 0.0 5.9 3 ; dih C25 C24 C23 C22
>
> 45 44 43 42 1 0.0 5.9 3 0.0 5.9 3 ; dih C26 C25 C24 C23
>
> 46 45 44 43 1 0.0 5.9 3 0.0 5.9 3 ; dih C27 C26 C25 C24
>
> 47 46 45 44 1 0.0 5.9 3 0.0 5.9 3 ; dih C28 C27 C26 C25
>
> 48 47 46 45 1 0.0 5.9 3 0.0 5.9 3 ; dih C29 C28 C27 C26
>
> 49 48 47 46 1 0.0 5.9 3 0.0 5.9 3 ; dih C9 C29 C28 C27
>
> 50 49 48 47 1 0.0 5.9 3 0.0 5.9 3 ; dih C10 C9 C29 C28
>
>  
>
>  
>
> title = vals
>
> cpp = /usr/bin/cpp
>
> define = -DFLEXIBLE
>
> constraints = none
>
> integrator = steep
>
> dt = 0.002 ; ps !
>
> nsteps = 500
>
> nstlists = 10
>
> ns_type = grid
>
> rlist = 1.0
>
> coulombtype = PME
>
> rcoulomb = 1.0
>
> vdwtype = cut-off
>
> rvdw = 1.0
>
> fourierspacing = 0.12
>
> fourier_nx = 0
>
> fourier_ny = 0
>
> fourier_nz = 0
>
> pme_order = 4
>
> ewald_rtol = 1e-5
>
> optimize_fft = yes
>
> ;
>
> ; Energy minimizing
>
> ;
>
> emtol = 100.0
>
> emsteps = 0.01
>
>  
>
>
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-- 
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Justin A. Lemkul
Graduate Research Assistant
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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