[gmx-users] question

[s.ghasemlou]

در 2017-12-30 10:15، RAHUL SURESH نوشته است:

> On Sat, 30 Dec 2017 at 12:10 PM, s.ghasemlou <s.ghasemlou at ut.ac.ir> wrote: 
> thanks for your response 
> 
>> Hello every one,
>> 
>> After using the command "g_grompp -f em.mdp -c totalbox1.gro -p
>> topol.top -o ions.tpr" I get the error:
>> 
>> ERROR 1 [file topol.top, line 863]:
>> ERROR: The cut-off length is longer than half the shortest box vector
>> or
>> longer than the smallest box diagonal element. Increase the box size
>> or
>> decrease rlist.(my box vectors are 31.16343- 31.16343- 31.16343)
> 
> What is the cut off scheme and value..? 
> 
> below is the em.mdp file content I have used 
> 
> ; LINES STARTING WITH ';' ARE COMMENTS
> title  = Minimization ; Title of run 
> ; Parameters describing what to do, when to stop and what to save
> integrator = steep  ; Algorithm (steep = steepest descent minimization)
> emtol  = 1000.0   ; Stop minimization when the maximum force < 10.0 kJ/mol
> emstep      = 0.01      ; Energy step size
> nsteps  = 50000    ; Maximum number of (minimization) steps to perform
> energygrps = system ; Which energy group(s) to write to disk 
> ; 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  = 1.0  ; Cut-off for making neighbor list (short range forces)
> coulombtype = PME  ; Treatment of long range electrostatic interactions
> rcoulomb = 1.0  ; long range electrostatic cut-off
> rvdw  = 1.0  ; long range Van der Waals cut-off
> pbc         = xyz   ; Periodic Boundary Conditions (yes/no) 
> 
>> I have tried different rlist, r columb and rvdw values. I have also
>> changed the box vector several times, but I still get the same error. I
>> don't know how to change them to fix the error.
>> 
>> There is also the below warning:
>> 
>> Warning: atom name 1 in topol.top and totalbox1.gro does not match (H55
>> - OW)
>> Warning: atom name 2 in topol.top and totalbox1.gro does not match (C2 -
>> HW1)
>> Warning: atom name 3 in topol.top and totalbox1.gro does not match (H53
>> - HW2)
>> Warning: atom name 4 in topol.top and totalbox1.gro does not match (H54
>> - OW)
>> Warning: atom name 5 in topol.top and totalbox1.gro does not match (C1 -
>> HW1)
>> Warning: atom name 6 in topol.top and totalbox1.gro does not match (H51
>> - HW2)
>> Warning: atom name 7 in topol.top and totalbox1.gro does not match (H52
>> - OW)
>> Warning: atom name 8 in topol.top and totalbox1.gro does not match (C50
>> - HW1)
>> Warning: atom name 9 in topol.top and totalbox1.gro does not match (H109
>> - HW2)
>> Warning: atom name 10 in topol.top and totalbox1.gro does not match
>> (H110 - OW)
>> Warning: atom name 11 in topol.top and totalbox1.gro does not match (O43
>> - HW1)
>> Warning: atom name 12 in topol.top and totalbox1.gro does not match (C42
>> - HW2)
>> Warning: atom name 13 in topol.top and totalbox1.gro does not match (C44
>> - OW)
>> Warning: atom name 14 in topol.top and totalbox1.gro does not match (C40
>> - HW1)
>> Warning: atom name 15 in topol.top and totalbox1.gro does not match (C41
>> - HW2)
>> Warning: atom name 16 in topol.top and totalbox1.gro does not match
>> (H100 - OW)
>> Warning: atom name 17 in topol.top and totalbox1.gro does not match (C46
>> - HW1)
>> Warning: atom name 18 in topol.top and totalbox1.gro does not match
>> (H102 - HW2)
>> Warning: atom name 19 in topol.top and totalbox1.gro does not match (C45
>> - OW)
>> Warning: atom name 20 in topol.top and totalbox1.gro does not match
>> (H101 - HW1)
>> (more than 20 non-matching atom names)
>> WARNING 1 [file topol.top, line 863]:
>> 32798 non-matching atom names
>> atom names from topol.top will be used
>> atom names from totalbox1.gro will be ignored
> 
> You can use maxwarn flag.... or change the cane in toolbox.gro 
> would you please tell me what the cane is in a .gro file? because using maxwarn flag didn't fix it.
> 
>> As I checked both the .gro and topol.top contents, atom names are the
>> same but here atom names of solvent water are mixed with atom names of
>> the ligand I used.
> 
> Someone else would definitely help you in This.
> 
>> please help me on this. Thanks in advance.
>> --
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> -- 
> *Regards,*
> *Rahul Suresh*
> *Research Scholar*
> *Bharathiar University*
> *Coimbatore*