Dear Justin.
Thanks for your kind advise.
But why don't it is not possible to apply the constant force which should
increases linearly (at each instant of time delta)
like at
t1 -f1
t2-f2
.
.
tn-fn
and corresponding to that force we get extension for each increment of
time in Gromacs. This is m
Dear Prof. van der Spoel,
Thanks for your reply. I tried touse the following commands (2 OpenMP threads):
gmx_mpi grompp -f eq.mdp -c em.gro-p swm4-dp.top -r posre.gro -o eq.tpr
mpirun -np 1 gmx_mpi mdrun -ntomp 2-deffnm eq
but this gave me the following errormessage in GROMACS 2018.2:
Hi,
It's possible, but there is no code written for it.
Mark
On Mon, Aug 13, 2018, 12:47 Rakesh Mishra wrote:
> Dear Justin.
>
> Thanks for your kind advise.
> But why don't it is not possible to apply the constant force which should
> increases linearly (at each instant of time delta)
> lik
Dear Mark,
Could you please comment on my previous question? I would really appreciate
it.
Best regards,
Mahsa
On Sat, Aug 11, 2018 at 12:52 PM, Mahsa wrote:
> Hi Mark,
>
> Thank you for your reply!
>
> I tried gmx make_ndx -f topol.tpr -o index.ndx before and then selected
> based on the ato
Hello Mark,
Thank for your clarification. Gromacs pulling has simple protocol for
pulling
using umbrella sampling. Where one can only get f/t and x/t . here t is
linearly
increases for both cases of force and distance. That actually not full fill
the need of
experimental pulling.
On Mon, Aug 13
On 8/13/18 6:38 AM, Rakesh Mishra wrote:
Hello Mark,
Thank for your clarification. Gromacs pulling has simple protocol for
pulling
using umbrella sampling. Where one can only get f/t and x/t . here t is
linearly
increases for both cases of force and distance. That actually not full fill
the
Hi,
Can you please share a link to something that indicates why this would be a
good tool for modeling such experimental pulling scenarios? Making the case
for implementing such a feature would benefit from that.
Mark
On Mon, Aug 13, 2018, 13:42 Rakesh Mishra wrote:
> Hello Mark,
>
> Thank for
Hi,
You need a composite selection, eg of an atomtype and residue type or
molecule type. Make a selection of the atomtype and another of whatever
seems suitable, and combine them.
Mark
On Sat, Aug 11, 2018, 13:53 Mahsa wrote:
> Hi Mark,
>
> Thank you for your reply!
>
> I tried gmx make_ndx -
Dear All,
I studied the interactions between BMP-2 (protein) and hydroxyapatite (HAP,
inorganic material) by GROMACS with the OPLS-AA force field. The mixing rule
was the Lorentz-Berthelot combination. A reviewer commented that 'The
interaction of organic molecule on inorganic material needs
Hi,
What experimental data can you replicate to show the model is valid?
Mark
On Mon, Aug 13, 2018, 17:34 Baolin Huang wrote:
> Dear All,
>I studied the interactions between BMP-2 (protein) and hydroxyapatite
> (HAP, inorganic material) by GROMACS with the OPLS-AA force field. The
> mixing
Hi,
I calculated the interaction energy(actually van der Waals part and
electrostatic part),Rg,RMSD,and RMSF.
regards,
--
该邮件从移动设备发送
--原始邮件--
发件人:"Mark Abraham ";
发送时间:2018年8月13日(星期一) 晚上11:02
收件人:"gmx-users" ;
抄送:"gromacs.org_gmx-users ";
主题:Re: [gmx-users] Mixing
On 8/13/18 11:28 AM, Baolin Huang wrote:
Hi,
I calculated the interaction energy(actually van der Waals part and
electrostatic part),Rg,RMSD,and RMSF.
regards,
I wouldn't think any of those are necessarily meaningful (interaction
energy almost certainly isn't, and a decomposition between vd
Hi all,
That is a pure simulation work,no experimental data. The reviewer doubt the
Lorentz-Berthelot combination rule for calculating the interaction energy
between BMP-2 and HAP. I have to persuade the reviewer that the mixing rule
works well in the BMP-2/HAP system.
Thanks for your help.
Baol
On 8/13/18 11:47 AM, Baolin Huang wrote:
Hi all,
That is a pure simulation work,no experimental data. The reviewer doubt the
Lorentz-Berthelot combination rule for calculating the interaction energy
between BMP-2 and HAP. I have to persuade the reviewer that the mixing rule
works well in the
Hi! I want to using GROMACS on my PC(Mac OS).
There is an error in the installation of “make" process.
My computer has 3.2GHz Intel Xeon W processor and Radeon Pro Vega 56 8176MB
GPU. (iMac pro default)
1) My computer is appropriate for GROMACS?
2) Can I use GPU for mdrun?
If it’s possible, I
Hi,
There's a fundamental difference between a a calculation and a simulation,
which is that the latter can defend its claim to model reality. Anybody can
put parameters into an equation.
Mark
On Mon, Aug 13, 2018, 18:49 Justin Lemkul wrote:
>
>
> On 8/13/18 11:47 AM, Baolin Huang wrote:
> > H
Hi,
You can probably get GPU support via the OpenCL implementation in GROMACS.
Check out the installation guide, and get the most recent version of
everything.
Mark
On Mon, Aug 13, 2018, 20:18 김나연 wrote:
> Hi! I want to using GROMACS on my PC(Mac OS).
> There is an error in the installation of
Dear gromacs users
For fixing PBC problem, I used following command:
gmx_mpi trjconv -f md.trr -s md.tpr -n index.ndx -o new.xtc -pbc nojump
But I encountered with:
Program gmx trjconv, VERSION 5.1.3
Source code file:
/root/gromacs_source/gromacs-5.1.3/src/gromacs/utility/futil.cpp, line: 469
Den 2018-08-13 kl. 11:49, skrev Chi Yuen Pak:
Dear Prof. van der Spoel,
Thanks for your reply. I tried touse the following commands (2 OpenMP threads):
gmx_mpi grompp -f eq.mdp -c em.gro-p swm4-dp.top -r posre.gro -o eq.tpr
mpirun -np 1 gmx_mpi mdrun -ntomp 2-deffnm eq
Did you try with
Den 2018-08-13 kl. 20:56, skrev Andrew Bostick:
Dear gromacs users
For fixing PBC problem, I used following command:
gmx_mpi trjconv -f md.trr -s md.tpr -n index.ndx -o new.xtc -pbc nojump
But I encountered with:
Program gmx trjconv, VERSION 5.1.3
Source code file:
/root/gromacs_source/groma
Hello,
This is telling you that the OPLS-AA force field does not have the dihedral
force-field parameters for your molecule (topol_Other_chain_C.itp) of the
Ryckaert-Bell type. Your exact problem might be:
(1) There is something wrong with the molecule topology.
(2) OPLS-AA really doesn't have the
Thank you for your reply!
Best regards,
Mahsa
On Mon, Aug 13, 2018 at 2:47 PM, Mark Abraham
wrote:
> Hi,
>
> You need a composite selection, eg of an atomtype and residue type or
> molecule type. Make a selection of the atomtype and another of whatever
> seems suitable, and combine them.
>
> Ma
Dear All:
I am doing umbrella sampling for a dimer (Consist of two molecules
stacking together, no physical bond). I tried different force constants,
I got different PMF for each of them. Could you suggest me, How reliably
can I choose force constant. Followings are the settings:
; Pull code
p
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