Thank you for the tip. I will try to use it.
Amit
On Fri, Oct 9, 2009 at 6:10 PM, Justin A. Lemkul wrote:
>
>
> Amit Choubey wrote:
>
>> Hi Justin,
>>
>> Yes you are right. I didnt fix the periodicity to start with. Could you
>> tell me how to do that, which command to work with?
>> Thanks.
>>
>
Amit Choubey wrote:
Hi Justin,
Yes you are right. I didnt fix the periodicity to start with. Could you
tell me how to do that, which command to work with?
Thanks.
Periodicity is corrected using trjconv. This involves creating a .tpr file of
to represent the system and using trjconv -pbc
Hi Mark,
Yes i checked the procedure on the original structure. It woks fine. As for
genconf i used the following
genconf -f dppc128.pdb -o out.gro -nbox 2 2 1
As Justin pointed out, I did not correct the periodicity of original
structure before using genconf .
Thank you,
Amit
On Fri, Oct 9, 20
Hi Justin,
Yes you are right. I didnt fix the periodicity to start with. Could you tell
me how to do that, which command to work with?
Thanks.
amit
On Fri, Oct 9, 2009 at 5:39 PM, Justin A. Lemkul wrote:
>
>
> Amit Choubey wrote:
>
>> Dear Gromacs Users,
>>
>> I have been trying to generate a l
Amit Choubey wrote:
Dear Gromacs Users,
I have been trying to generate a larger lipid system but am running into
troubles due to improper initial co-ordinates set up. Following are the
steps i am trying to follow.
1. I start with a 128 dppc membrane and use genconf to create a larger
system
Amit Choubey wrote:
Dear Gromacs Users,
I have been trying to generate a larger lipid system but am running into
troubles due to improper initial co-ordinates set up. Following are the
steps i am trying to follow.
1. I start with a 128 dppc membrane and use genconf to create a larger
syst
Dear Gromacs Users,
I have been trying to generate a larger lipid system but am running into
troubles due to improper initial co-ordinates set up. Following are the
steps i am trying to follow.
1. I start with a 128 dppc membrane and use genconf to create a larger
system. I got the dppc128.pdb fro
João M. Damas wrote:
What do you mean by mutually inconsistent? From what I understand, they
aren't.
I mean a set for which there is no molecular arrangement that satisfies.
Also, [bonds] type 6 won't work for what I want, since I don't want to
keep the molecules at a fixed distance but to pr
What do you mean by mutually inconsistent? From what I understand, they
aren't.
Also, [bonds] type 6 won't work for what I want, since I don't want to keep
the molecules at a fixed distance but to prevent them from coming closer,
i.e. I want a potential that depends on the distance between the ato
Yongchul Chung wrote:
After EM, I got:
Potential Energy = 1.7242092e+05
Maximum force = 2.1079963e+03 on atom 675
Norm of force = 5.9417034e+01
I think my system size is too big compared to the box size so I am going
to run the simulation with smaller number of molecules to see w
After EM, I got:
Potential Energy = 1.7242092e+05
Maximum force = 2.1079963e+03 on atom 675
Norm of force = 5.9417034e+01
I think my system size is too big compared to the box size so I am going to
run the simulation with smaller number of molecules to see whether this
helps or not.
Yongchul Chung wrote:
yes I carried out energy minimization and used following parameters.
OK, so what values of potential energy and maximum force did EM achieve?
-Justin
title = FWS
cpp = /usr/bin/cpp ; the c pre-processor
define = -DFLEXIB
Yongchul Chung wrote:
Hi again gmx-users,
I ran into LINCS error again when I tried to incorporate pressure
scaling parameters.
It seems like the initial pressure and temperature is erroneously large
as shown in the md.log file below. can anyone tell me how to fix this?
Did you run energ
Hi,
If you use -pi with g_mindist, all the other output options are ignored.
Berk
> Date: Fri, 9 Oct 2009 14:24:00 +0200
> From: cseif...@bph.ruhr-uni-bochum.de
> To: gmx-users@gromacs.org
> Subject: [gmx-users] g_mindist
>
> Dear Mr. Gromacs, ;-)
> and hello to everybody!
>
> When I use g_mi
Hi,
I would like to simulate hard sphere with different
charge values (e.g. +30), with different diameters (e.g. 5 nm)
and with different values of Lennard-Jones.
In addiction, in these models of the hard sphere
I would like to insert dipole (e.g. 15 Debye).
So, is this possible to simulate
Hi,
I would like to simulate hard sphere with different charge values (e.g. +30)
and with different diameters (e.g. 5 nm). In addiction, in these models of the
hard sphere I would like to insert dipole (e.g. 15 Debye). So, is this possible
to simulate these models in GROMACS?
Thanks,
Pos-doc.
Hi,
Unfortunately this is not possible.
If you do not have to many pairs, you can change all (or all minus one type)
from pairs to tabulated bonds (bonds type 9) in your topology.
Then you can supply as many different bond tables as you like.
Note that this will supply a single potential though,
Dear Mr. Gromacs, ;-)
and hello to everybody!
When I use g_mindist with a Syntax like this:
g_mindist -f ./prot.xtc -s ./prot.tpr -n ./prot.ndx
-od ./protein_self.xvg -o prot.out -pi
Then I just get the xvg file with the distance of the group (I selected
C-alphas) with its periodic image. The xvg
I think there must be a way in gromacs to pass tabulated potenttial for 1-4
interaction for two groups as interaction between different pairs can be
significantly different and can change the structure of an indiviual molecule.
I would request: Please let me know if it is possible to pass tabul
ms wrote:
Justin A. Lemkul ha scritto:
My aim is to re-implement a formerly standalone CG model by mean of gmx.
It seems that gmx is well suited to the task; however I understand that
there is an incredible number of pitfalls where a newbie fall in.
I am currently reading and re-reading the m
Justin A. Lemkul ha scritto:
>> My aim is to re-implement a formerly standalone CG model by mean of gmx.
>> It seems that gmx is well suited to the task; however I understand that
>> there is an incredible number of pitfalls where a newbie fall in.
>>
>> I am currently reading and re-reading the ma
ms wrote:
Hi,
First of all, I am new to Gromacs and quite new to the MD field (I had a
read of the Daan-Frenkel book and played very little with custom CG
models - I used to be an experimental guy), so please bear with me if
questions happen to be naive.
My aim is to re-implement a formerly s
Hi,
First of all, I am new to Gromacs and quite new to the MD field (I had a
read of the Daan-Frenkel book and played very little with custom CG
models - I used to be an experimental guy), so please bear with me if
questions happen to be naive.
My aim is to re-implement a formerly standalone CG m
OK, I'll answer once more.
You are apparently convinced you are doing the right thing.
But if you have a problem and want someone to help you,
you should report all warnings you get so users do not waste their time
(and your time) helping you. Mentioning this warning right away
would have s
I asked your help since my tabulated potential reports in the third column the
derivatives (minus the derivatives...to be precise) which are analitically
exact with respect to the potential reported in the second column. So, in this
case, these are the exact forces. If the numerical derivatives
b95203...@ntu.edu.tw wrote:
Hi all,
I have some pdb file of peptides that I wish to do free energy calcuation.
Is there any source I can do that?
http://www.gromacs.org/Documentation/How-tos/Free_Energy_Calculations
If you want a more specific answer, ask a more specific question.
-Justin
subarna thakur wrote:
Hello
I want to analyze the RMSF fluctuation of each residue of a protein
during a simulation run. I am giving the command
g_rmsf -f md.xtc -s md.tpr -b 4000 -e 6000 -o traj_rmsf.xvg -ox
traj_avg.pdb. Then I am selecting the whole protein for the analysis. I
am getting
Hi,
I ran your system and mdrun prints a VERY clear warning to stderr and to md.log:
WARNING: For the 999 non-zero entries for table 0 in table_b0.xvg the
forces deviate on average 164% from minus the numerical derivative of
the potential
I understand that Gromacs can be somewhat complicated fo
Hi all,
I have some pdb file of peptides that I wish to do free energy calcuation.
Is there any source I can do that?
Thanks
Regards,
William
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Please
>x2top -h
>Did you use the -alldih flag? For OPLS like force field all dihedrals
are need, for gromos like ff only one dihedral per bond is kept, that is
>why.
Thanks, David. I did not use -alldih. After I used it, four dihedrals
for one bond are all kept. Anyway I have got this point about th
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