On 10/02/2012 5:11 AM, GZ Zhang wrote:
Hi, ALL
We are writing our own MD program to simulate water and the TIP4P
model is being considered.
I am wondering that how does GROMACS program handle the force on the
massless M site of the TIP4P
model? It would be better to be informed the algorit
On 10/02/2012 1:20 PM, bharat gupta wrote:
Hi,
I am planning to carry out a REMD study on a 12 residue beta-hairpin
peptide. I have read the gromacs tutorial for that . I have certain
doubts regarding the tutorial :-
1. Step. 4 says that "run short simulations to have an estimate of the
exc
On 10/02/2012 4:41 PM, vivek sharma wrote:
Hi Justin,
Thanks for your response. After posting my query, I tried running the
similar set with
NPT run for 100 ps with sd integrator (with Pcoupl = berensen, tau_p
= 0.5, compressibility = 4.5e-05, ref_p = 1.0)
On giving berendsen instead of Parrine
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Hi Justin,
Thanks for your response. After posting my query, I tried running the
similar set with
NPT run for 100 ps with sd integrator (with Pcoupl = berensen, tau_p
= 0.5, compressibility = 4.5e-05, ref_p = 1.0)
On giving berendsen instead of Parrinello-Rahman for pressure
coupling, job finished
Hi Rohit,
Have you checked the atoms around 3460? It seems there's something wrong
with your starting structure.
Cheers,
Tsjerk
On Feb 9, 2012 2:09 PM, wrote:
Hi Lina,
I am sorry, I think I forgot to mention that I did perform energy
minimisation using Steep-Descent for 5000 steps, before NV
Hi,
I am planning to carry out a REMD study on a 12 residue beta-hairpin
peptide. I have read the gromacs tutorial for that . I have certain doubts
regarding the tutorial :-
1. Step. 4 says that "run short simulations to have an estimate of the
exchange rate (can get a good estimate within ~100 p
Hi all,
Can you please guide me how one can calculate fraction of gauche+ and
gauche- defects in the center of a polymer chain?
Appreciate you help.
Juliete
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francesca vitalini wrote:
Tryed the double precision without any success... Again the same type of
error message. Might need to try other minimization algorithm. Any
suggestions on that?
What is the Fmax you achieve, and what are your intents for this process?
Minimizing very low is only
Hi, ALL
We are writing our own MD program to simulate water and the TIP4P model
is being considered.
I am wondering that how does GROMACS program handle the force on the
massless M site of the TIP4P
model? It would be better to be informed the algorithm(or the code in
GROMACS). Thanks.
Gu
Tryed the double precision without any success... Again the same type of
error message. Might need to try other minimization algorithm. Any
suggestions on that?
2012/2/9 Justin A. Lemkul
>
>
> francesca vitalini wrote:
>
>> Hi all!
>> I'm trying to run some energy minimization with gromacs 3.3.1
--- On Mon, 6/2/12, Ignacio Fernández Galván wrote:
> The .gro file does not contain any mention to "ACX", but I
> believe it's not needed, as long as it's in the .top,
> right?
It seems that default group names are generated not from moleculetype names,
but from residue names. At least that's
francesca vitalini wrote:
Hi all!
I'm trying to run some energy minimization with gromacs 3.3.1 on a
system that I have transformed from cg to aa. After the reverse
transformation I solvate the system and I try to minimize just the
proteins (my system is a dimer) keeping fixed the water. The
Hi all!
I'm trying to run some energy minimization with gromacs 3.3.1 on a system
that I have transformed from cg to aa. After the reverse transformation I
solvate the system and I try to minimize just the proteins (my system is a
dimer) keeping fixed the water. Then the idea would be to minimize t
By setting the emtol to 1.0, didnt work. Anyother way i could figure out.
On Thu, Feb 9, 2012 at 6:32 PM, Justin A. Lemkul wrote:
>
>
> lina wrote:
>
>> On Thu, Feb 9, 2012 at 6:17 PM, aiswarya pawar
>> wrote:
>>
>>> Dear Gromacs users,
>>>
>>> I have a MD simulated protein and i take frame fro
Hi Lina,
I am sorry, I think I forgot to mention that I did perform energy
minimisation using Steep-Descent for 5000 steps, before NVT.
I was so engrossed in other details that I forgot to mention it!
Quoting lina :
On Thu, Feb 9, 2012 at 8:44 PM, wrote:
Dear Gromacs users,
I have be
vivek sharma wrote:
Hi There,
I was trying to run a equilibrium run (npt) for system of "Methane in
1-octanol" (1 methane molecule with 200 1-octanol molecules with OPLS FF
parameters). Following is the series of steps I followed:
1. Energy minimization with steep integrator for 5000 steps
lina wrote:
On Thu, Feb 9, 2012 at 6:17 PM, aiswarya pawar wrote:
Dear Gromacs users,
I have a MD simulated protein and i take frame from this and remove water
and add water implicit in the interface and want to do energy minimization
but while doing the minimization i get errors. The steps
Dear Gromacs users,
I have a MD simulated protein and i take frame from this and remove water
and add water implicit in the interface and want to do energy minimization
but while doing the minimization i get errors. The steps followed are-
pdb2gmx -ignh -f 1OC0.pdb -o 1oco.pdb -p 1oco.top -nocmap
On Thu, Feb 9, 2012 at 6:17 PM, aiswarya pawar wrote:
>
> Dear Gromacs users,
>
> I have a MD simulated protein and i take frame from this and remove water
> and add water implicit in the interface and want to do energy minimization
> but while doing the minimization i get errors. The steps follow
On Thu, Feb 9, 2012 at 7:25 PM, Kiwoong Kim wrote:
> Hi,
>
> I have a simulation result from 0 to 50ns after equilibration run.
> I want to divide this data set equally into 10blocks (10ns each) and get
> block averaged MSD curve (average of 10 blocks).
I would try some external software. excel.
On Thu, Feb 9, 2012 at 8:44 PM, wrote:
> Dear Gromacs users,
>
> I have been trying to simulate a Protein-DNA complex using gromacs, but each
> time I have been facing problems. I would like to point out that both the
> Protein and DNA have been modeled and after that docked in order to obtain a
Dear Gromacs users,
I have been trying to simulate a Protein-DNA complex using gromacs,
but each time I have been facing problems. I would like to point out
that both the Protein and DNA have been modeled and after that docked
in order to obtain a complex. Following are the parameters I am
Hi,
I have a simulation result from 0 to 50ns after equilibration run.
I want to divide this data set equally into 10blocks (10ns each) and get
block averaged MSD curve (average of 10 blocks).
It seems that I mange to get block MSD data by using g_msd -beginfit 0
-endfit 10, g_msd -beginfit 10 -
Hello
Could you please clarify what is the reason for adopting the "all-bonds"
constraints as a standard practice in gmx protein simulations?
I mean, the argument that "the time step in molecular simulations can be
increased by a factor of 4 by replacing the bond vibrations by holonomic
constrain
Dear Gromacs users,
I have a MD simulated protein and i take frame from this and remove water
and add water implicit in the interface and want to do energy minimization
but while doing the minimization i get errors. The steps followed are-
pdb2gmx -ignh -f 1OC0.pdb -o 1oco.pdb -p 1oco.top -nocmap
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