I am trying to simulate amorphous organic solid system with Parrinello-Rahman
at P=1 Bar. The maximal dt value which holds molecules together is 0.0008 and
it's increasing leads to evaporation. What may be incorrect?
Berendsen works well with dt=0.001 but it isn't recommended.
mdp options for p
Dear GROMACS users,
I want to use the geometric mean of both sigma (sigma i sigmaj)and
epsilon(epsilon i epsilon j) as a combination rule in my simulation.
According to the combination rules in the manual, the combination 3
incorporates Vii=sigma and Wii= epsilon along with geometric mean of Ci(6)
Dear all, Iam trying to add viscidity bond code to gromacsc 4.0.7. I found the
harmonic bond code in bondfree.c ,but i could not conform which source document
include the velocity information . Can somebody please advise me on how to
overcome this issue?Thank you. Regards, jieliu
--
Gromacs Us
Dear all, Iam trying to add viscidity bond code to gromacsc 4.0.7. I found the
harmonic bond code in bondfree.c ,but i could not conform which source document
include the velocity information . Can somebody please advise me on how to
overcome this issue?Thank you. Regards, jieliu
--
Grom
On 3/20/18 7:15 PM, Alex wrote:
Thanks Justin.
On Tue, Mar 20, 2018 at 3:02 PM, Justin Lemkul wrote:
On 3/20/18 2:40 PM, Alex wrote:
Dear all,
The potential energy of my system after two minimization steps (with and
without constrained) is converging well, however, it is still positive
Thanks Justin.
On Tue, Mar 20, 2018 at 3:02 PM, Justin Lemkul wrote:
>
>
> On 3/20/18 2:40 PM, Alex wrote:
>
>> Dear all,
>>
>> The potential energy of my system after two minimization steps (with and
>> without constrained) is converging well, however, it is still positive
>> around 1000 kj/mol
On 3/20/18 6:06 PM, Alex wrote:
On Mon, Mar 19, 2018 at 8:57 PM, Justin Lemkul wrote:
On 3/19/18 8:15 PM, Alex wrote:
Dear all,
Using topolbuild I can generate the case.gro, case.top, ffcase.itp and
posrecase.itp out of a case.mol2 which contain only a single molecule of
X.
Also, using
On Mon, Mar 19, 2018 at 8:57 PM, Justin Lemkul wrote:
>
>
> On 3/19/18 8:15 PM, Alex wrote:
>
>> Dear all,
>>
>> Using topolbuild I can generate the case.gro, case.top, ffcase.itp and
>> posrecase.itp out of a case.mol2 which contain only a single molecule of
>> X.
>>
>> Also, using the "gmx inse
Thanks everyone for your reply.
I see your point that it could just be some error cancellation from
constraints and parameters.
I was previously using gromacs-5.1.4, and changed to gromacs-2018, and the
drift seems to be much smaller! I get something similar to what Mark had
posted -0.25 kJ/mo
Hello all,
I have run a simulation for 10 ns (0.001 * 1000 = 1 ps) and have
saved the data for every 0.5 ps (nstxout= 500etc.,...) (which comes to
2 frames...).
Since if i extract the trajectory in .gro format for the full simulation,it
will be such a huge file, so i intended to ex
On 3/20/18 2:40 PM, Alex wrote:
Dear all,
The potential energy of my system after two minimization steps (with and
without constrained) is converging well, however, it is still positive
around 1000 kj/mol !
I think it is not a good sign for my system, but, what could be the reason
and how I ca
Dear all,
The potential energy of my system after two minimization steps (with and
without constrained) is converging well, however, it is still positive
around 1000 kj/mol !
I think it is not a good sign for my system, but, what could be the reason
and how I can overcome the issue? The system gen
Prior to generating the topology (say, with x2top) use editconf on your
coordinates to put the crystal in a box of size that's compatible with
the periodicity and the number of unit cells in your crystal sample.
Alex
On 3/20/2018 10:49 AM, Bala subramanian wrote:
Dear Grom. users,
Greetings,
Dear Grom. users,
Greetings,
I have to simulate a crystal lattice with gromacs. In the unit cell, there
are 16 copies of the mineral (Lets say 16 residues). If all residues have
the same number of atoms, I can simply create the .rtp file for one residue
and then proceed for the topology generatio
Dear GROMACS users,
I want to use the geometric mean of both sigma (sigma i sigmaj)and
epsilon(epsilon i epsilon j) as a combination rule in my simulation.
According to the combination rules in the manual, the combination 3
incorporates Vii=sigma and Wii= epsilon along with geometric mean of Ci(6)
Dear Wes,
Thanks for clarifying, I did as you told and it worked. The resulting
dG_hyd of NH4+ is -62.5 kJ/mol, while the experimental value is -285 kJ/mol
(10.1039/FT9918702995). I am using OPLS and SPC/E water. Energy values of
the last lambdas showed higher error bars, so now I am refining the
On Tue, Mar 20, 2018 at 2:30 AM, rose rahmani wrote:
> Hi,
> I want to extract a structure in a box, i mean i want to extract a sheet
> from the box of solution, because i dont have any separated .gro file from
> my sheet. How can i do that?
>
Try creating an index file using "gmx make_ndx" to c
Dear Mark sir,
Thank you... I will try with the later versions.
I am actually using modified version of gromacs-4.6.2[by J S Hub et al.,] ,
for calculating swaxs(small and wide angle x ray scattering) profiles and
swaxs driven MD.
I will learn to incorporate swaxs driven MD to later versions with y
Dear gmx-users
I am trying to calculate free energy of VDW transformation. The system is
very simple as I want to test the methodology. Single neutral LJ particle
is transformed from state A to state B in TIP4P water.
I have tried simulations with different state B LJ parameters without
changing
19 matches
Mail list logo
