[gmx-users] lipid restrain

[RINU KHATTRI]

hello every one
i got the solution it s not for -nt its for X we have to use core of
workstation and in my system it is 4
so command is

mdrun -nt 4 -deffnm npt and its working



On Sat, Jul 26, 2014 at 12:41 PM, RINU KHATTRI <nickname.mittu at gmail.com>
wrote:

> hello everyone
> its working simply add D flag in .itp file
> but got anothe error in equilibrium2
>
> gmx mdrun -nt X -deffnm npt
>
> i used this command
>
> and getting Expected an integer argument for option -nt
>
> kindly help
>
>
>
>
> On Sat, Jul 26, 2014 at 12:15 PM, RINU KHATTRI <nickname.mittu at gmail.com>
> wrote:
>
>> hello every one
>> i am working on complex with POPC membrane i want to use position
>> restrain in lipid but it is not working it's give error
>>  file lipid_posre.itp, line 57 ]:
>> Atom index (53) in position_restraints out of bounds (1-52).
>> this probably means that you have inserted topology section
>> "position_restraints"
>> in a part belonging to a different molecule than you intended to.
>> last line sof my topology file is
>> ; Include Position restraint file
>> #ifdef POSRES
>> #include "posre.itp"
>> #endif
>>
>> ; Include ligand topology
>> #include "epi.itp"
>>
>> ; Include Position restraint file for UNK
>> #ifdef DPOSRES_UNK
>> #include "posre_unk.itp"
>> #endif
>>
>> ; Include POPC side chain topology
>> #include "popc.itp"
>>
>> ; Include Position restraint file for lipid
>> #ifdef DPOSRES_LIPID
>> #include "lipid_posre.itp"
>> #endif
>>
>> ; Include water topology
>> #include "gromos43a1_lipid.ff/spc.itp"
>>
>> #ifdef POSRES_WATER
>> ; Position restraint for each water oxygen
>> [ position_restraints ]
>> ;  i funct       fcx        fcy        fcz
>>    1    1       1000       1000       1000
>> #endif
>> [moleculetype]
>> POPC
>> #ifdef DPOSRES_LIPID
>> [ position_restraints ]
>> ; i  funct  fcx    fcy    fcz
>>    8    1    1000000   1000000   100000   ; restrains to a point x,y,z
>>
>> #endif
>>
>> ; Include topology for ions
>> #include "gromos43a1_lipid.ff/ions.itp"
>>
>> [ system ]
>> ; Name
>> Displayed atoms in water
>>
>> [ molecules ]
>> ; Compound        #mols
>> Protein_chain_A     1
>> UNK    1
>> POPC    122
>> SOL    9410
>> CL    15
>> my min.mdp is
>> define        = -DPOSRES_LIPID -DPOSRES -DPOSRES_UNK   ;position restrain
>> on protein  ligand and POPC
>>
>
>