Dear Gromacs users,
Please somebody help .
editconf computs the incorrect value of "mass of input". I tried to resolve
this problem but failed. Previously I was doing AOt but now I just found that
the molecule OS1 =O2L showing error . Here I posted my A.pdb, RM.rtp
atomtypes.atp. The mass of
Dear Gromacs users,
Please somebody help .
editconf computs the incorrect value of "mass of input". I tried to resolve
this problem but failed. Previously I was doing AOt but now I just found that
the molecule OS1 =O2L showing error . Here I posted my A.pdb, RM.rtp
atomtypes.atp. The mass of
p is there and which contains the atom names which I posted last
email
Thanks for your regard
Hari
On Monday, October 28, 2013 4:50 PM, Justin Lemkul wrote:
On 10/28/13 7:41 PM, Hari Pandey wrote:
>
>
>
>
> Thank you so much Mark.
>
> I still did not understand. Mo
Thank you so much Mark.
I still did not understand. More detaily. Atomtypes are only following:
atomtypes.atp::
H 1.00800 ; polar H
DUM 0.0 ; dummy atom
HAL1 1.008000 ; alphatic proton
HAL2 1.008000 ; alphatic proton
HAL3 1.008000 ;
Dear Gromacs Users,
First, I would like to thank Dr. Lemkul for reply.
My problem description is as follows:
I am using CHARMM36 forcefield to equilibrate of AOT. when I add the mass of
all atoms from topology, it gives me 444.5 which is correct but when I run the
script
editconf -c -f A.gro
Hi GROMACS users
can any body tell me how do I solvate fixed number of molecules in fixed
volume: for example 100 molecule water in 14*14*14 Aungstrom^3 box. eidt conf
and genbox never can do this.
One more question.
Please any body help me on following warning:
WARNING: masses and atomic (
Hi Gromaxers,
Thanks for previous answers.
I have to simulate reverse micelle after solvation with isooctane.My system now
is:
ISOOCTANE(solvent)+AOT(surfactant)+coreWATER.
When I do grompp, it says moleculetype SOL is redefined and lo
Hi all GROMACS users,
I need to make a pdb file of AOT reverse micell . Please some body tell me how
do I build it and which package would best for this work. Now I am using
PACKMOL but it seems just a geometrical mathematical manipulation. I want to
arrange charge, LJ parameter, hydrogen bond
Hi GROMACS users,
Could you please somebody tell me how do I solvate A Reverse Micell by fixed
(200) molecule of water keeping in fixed annular region around it. That is how
do I solvate spherical micell by water so that the width of spherical region
around it is fixed?
lots of thanks for help
Hi all gromacs users,
I have new forcefield and I have this folder in my working directory as well as
in /share/gromacs/top. When I run pdb2gmx from head node this forcefield
appears in list but when I run from slave nodes it do not appear in pdb2gmx
list. could somebody tell me how do resolve
Hi all GROMACS users
I added a new forcefield folder to head node in
/opt/bio/gromacs/share/gromacs/top and it appears in the list of forcefield in
pdb2gmx while I run it from head node of cluster. But if I run pdb2gmx from
other slave nodes , it do not appear in the list.
So, Please could
Hi all gromacs users,
I am new to GROMACS , please help me
I have following (NVT.mdp) (NPT.mdp) and (NVE.mdp) . I have three parts of
system, A, B and C.
I want to put thermostat on A and C and couple the tempereture and do not put
any thermostat on B.
In gromacs I want to do Following:
Hi all gromacs users
I have following (NVT.mdp) (NPT.mdp) and (NVE.mdp) . I have three parts of
system, A, B and C.
I want to put thermostat on A and C and couple the tempereture and do not put
any thermostat on B.
What I want is: after some ps, temperature of A and C should be constant (
Hi ,
How do I solve this problem in GROMACS:
I have a system with 3 part A,B and C
I have to put thermostat for A and C but not for B.
Gromacs display error, what is temperature for B.
How do aI decouple part B
thanks for help
Hari
--
gmx-users mailing listgmx-users@gromacs.org
Dear Gromacs users,
I am a new user and I have some questions
I confused about indexing. in atomtypes.atp clearly we can know the index
is for what kind of atom but in ffbondedtype.itp there is different kind of
the indexing so I confused how do i pathch the force field .
Some are obvious
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