[gmx-users] KALP15 in DPPC

[negar habibzadeh]

hi . i am doing simulation of peptide in DOPC bilayer. i have dopc.itp ,
dopc.pdb, dopc.gro , peptide.itp , sample.top for dopc ,
peptide.pdb,topol.top. i used below commands.

gmx editconf -f peptide.gro -o pep.gro -box 6.35172   6.80701   7.49241 -c
(it corresponds to the x/y/z box vectors of the DOPC unit cell)
i merg peptide and dopc:
cat pep.gro DOPC_323K.gro > tot1.gro
(I remove unnecessary lines)
i add ions :
gmx grompp -f ions.mdp -c tot1.gro -p mem.top -o ions.tpr
gmx genion -s ions.tpr -o tot.gro -p mem.top -pname NA -nname CL -nn 8
i get tpr file  (in mem.mdp i add some line to freeze protein )
gmx grompp -f mem.mdp -c tot.gro -p mem.top -o mem.tpr -n index.ndx
and i use g-membed command:
g_membed -f mem.tpr -dat mem.dat -c final.gro -n index.ndx -xyinit 0.1 (in
mem.dat i include the place of protein in the center of box)
in final.gro there were a few stray water molecules, i deleted them
manually and
i did energy minimization :
gmx grompp -f minim.mdp -c final.gro -p mem.top -o em.tpr
gmx mdrun -v -deffnm em
i checked em.gro , every thing is ok . but when i run nvt
in nvt.gro , A large number of water molecules are inside the membrane.
how can i solve this problem ?

On Mon, Jan 22, 2018 at 4:19 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 1/21/18 1:23 PM, negar habibzadeh wrote:
>
>> hi . in vmd how can i find special number for each atom? i want to delete
>> those atoms from my gro file.
>>
>
> You can label atoms by clicking on them in label mode. If you have further
> questions about VMD, post to their mailing list.
>
> -Justin
>
>
> tnx
>>
>>
>> On Mon, Jan 15, 2018 at 9:12 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>> On 1/15/18 10:56 AM, negar habibzadeh wrote:
>>>
>>> tnx so much
>>>>    i got nvt.tpr and now i want to run it but i am getting this error :
>>>> Fatal error:
>>>> Too many LINCS warnings (5258)
>>>> If you know what you are doing you can adjust the lincs warning
>>>> threshold
>>>> in your mdp file
>>>> or set the environment variable GMX_MAXCONSTRWARN to -1,
>>>> but normally it is better to fix the problem
>>>>
>>>> I use position restraints on the lipid headgroups for P of DOPC . i add
>>>> the
>>>> following lines to the system topology after the #include "dopc.itp"
>>>> line.
>>>>
>>>> #include "DOPC.itp"
>>>>
>>>> #ifdef POSRES_LIPID
>>>> #include "lipid_posre.itp"
>>>> #endif
>>>>
>>>> and i add the following line in nvt.mdp :
>>>> define          = -DPOSRES_protein  -DPOSRES_LIPID  ; Position restraint
>>>> for each protein and for DOPC P
>>>>
>>>> i created lipid_posre.itp :
>>>>
>>>> ; position restraint file for DOPC P
>>>>
>>>> [ position_restraints ]
>>>> ;  i funct       fcx        fcy        fcz
>>>>      20    1       0       0       1000
>>>> ~
>>>>
>>>> i used position restraints for lipids but again when i want to run nvt
>>>> ,i
>>>> get this error :
>>>>
>>>> Fatal error:
>>>> Too many LINCS warnings (5258)
>>>> If you know what you are doing you can adjust the lincs warning
>>>> threshold
>>>> in your mdp file
>>>> or set the environment variable GMX_MAXCONSTRWARN to -1,
>>>> but normally it is better to fix the problem
>>>>
>>>> how can i solve this problem ?
>>>>
>>>> http://www.gromacs.org/Documentation/Terminology/Blowing_Up#
>>> Diagnosing_an_Unstable_System
>>>
>>> -Justin
>>>
>>>
>>> --
>>> ==================================================
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Assistant Professor
>>> Virginia Tech Department of Biochemistry
>>>
>>> 303 Engel Hall
>>> 340 West Campus Dr.
>>> Blacksburg, VA 24061
>>>
>>> jalemkul at vt.edu | (540) 231-3129
>>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>>
>>> ==================================================
>>>
>>> --
>>> Gromacs Users mailing list
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>>>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==================================================
>
> --
> Gromacs Users mailing list
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