Enemark Soeren wrote:
Ahh, now I understand - sorry, Omer!
In fact, I have compared all three single hydrogen RDFs and they are
identical and also relatively smooth. Since, however, with 3 times more
data points (all three hydrogen atoms taken together) I get a different
RDF, would that in
Ahh, now I understand - sorry, Omer!
In fact, I have compared all three single hydrogen RDFs and they are
identical and also relatively smooth. Since, however, with 3 times more
data points (all three hydrogen atoms taken together) I get a different
RDF, would that indicate that I do not have e
Hi everyone,
I have been trying to set up an "infinitely" hard potential wall.
I tried to use the available wall options and could not really get it to do
what i needed. I wanted a steep repulsive potential but when i created that,
the system was blowing up, reason being that it requires smaller t
Omar's response answered that question on why they are different. In
the first one you are grouping all three into one group, second is just
one of the hydrogen types. The fact that the rdf you get is different
indicates that all three hydrogens are not identical. Have you compared
the rdf for e
Baofu Qiao wrote:
HI all,
I have try the top2psf.tcl from Justin and the top2psf.pf from the VMD
website. But both of them can only deal with single chain system. Take
an example, if there are 10 proteins (+water) in my system, how to
convert to topology of the total system to .psf file? I t
ms wrote:
Hi Mark,
Thanks for your answer.
Mark Abraham ha scritto:
There's nothing directional about the physics of a hydrogen bond, unless
your model makes it so. There'd be nothing intrinsically valid or
invalid with that either, so long as you parameterized the force field
under that assum
青 叶 wrote:
I did a energy minimization on a system contain one [AuCl4]- and 503
water moleculars, by using a self-define non-bond interaction (which is
obtain from ab-initio calculation), my em.mdp file is as follow:
title = yqq
cpp= /usr/bin/cpp ; the c pre
jennifer johnston wrote:
Dear All,
I'm attempting to simulate a dimeric protein in an explicit
bilayer/water environment. I'd like to remove the translation & rotation
of one protomer relative to the other, so that one protomer is able to
move around relative to the stationary one. I'm using s
ram bio wrote:
Dear Justin,
Thanks for the suggestion and advice.
As i have used a modelled protein and want to obtain the lowest energy
configuration of the protein by doing dynamics,
That's all very well, but what will that give you other than a set where
the partition of total energy into
Dear All,
I'm attempting to simulate a dimeric protein in an explicit bilayer/water environment. I'd like to remove the translation & rotation of one protomer relative to the other, so that one protomer is able to move around relative to the stationary one. I'm using semiisotropic pressure coupling
Thanks allot for all your help
Arik
Justin A. Lemkul wrote:
Arik Cohen wrote:
Hi,
I'll be most thankful if someone could tell me how to run a
fragmented trajectory using only the mdrun command. As of now I'm
using :
while(SimuTime < SimTime)
{
...
system("tpbconv -s run.tpr
Arik Cohen wrote:
Hi,
I'll be most thankful if someone could tell me how to run a fragmented
trajectory using only the mdrun command. As of now I'm using :
while(SimuTime < SimTime)
{
...
system("tpbconv -s run.tpr -f run.trr -e run.edr -extend 1.0 -o
run.tpr");
system("md
Hi,
I'll be most thankful if someone could tell me how to run a fragmented
trajectory using only the mdrun command. As of now I'm using :
while(SimuTime < SimTime)
{
...
system("tpbconv -s run.tpr -f run.trr -e run.edr -extend 1.0 -o
run.tpr");
system("mdrun -cpi run.cpt -cpo
While using g_wham to obtain a PMF from umbrella sampling simulations I came
up with the following problem. I have simulated my windows with a 0.1nm
difference between structures starting from the initial position where my
dimer is equilibrated and ending 0.5nm farther than what the lennard jones
a
Hi Stefan,
If you know the bound state, you can use the double decoupling method
to decouple the bound state and then recouple into bulk solvent.
Note that both decoupling and umbrella sampling methods will require
that you make the appropriate corrections to standard state values and
tha
Hello.
I have finished calculating the PMF of dimerization for my system using
umbrella sampling and WHAM. But came up with some free energy values that
are not compatible to the ones found in other works. I have alread had
several instrutions and tips from Justin in past email here in gms users'
l
I did a energy minimization on a system contain one [AuCl4]- and 503 water
moleculars, by using a self-define non-bond interaction (which is obtain from
ab-initio calculation), my em.mdp file is as follow:
title = yqq
cpp = /usr/bin/cpp ; the c pre-processor
de
Hello everybody,
Here is the rtf file I mentioned previously. It can be used by PSFGEN to
generate a psf file from pdb files. The result can be used, for example,
by the PME Electrostatics plugin of VMD. PSFGEN is available as a VMD
plugin or as an independant executable.
Nicolas
Nicolas SA
Pablo Englebienne wrote:
OK, I started over with the CHCl3 box from scratch. I prepared the
following itp file from the CHCL3 parameters in ffG53a5.rtp:
---[chcl3.itp]---
[ moleculetype ]
; Namenrexcl
CHCL3 3
[ atoms ]
; nr type resnr residue atom cgnr
Dear Justin,
Thanks for the advice, will try to follow using grace.
Ram
On Wed, Oct 21, 2009 at 8:25 PM, Justin A. Lemkul wrote:
>
>
> ram bio wrote:
>>
>> Dear Justin.
>>
>> Thanks for the suggestion, definitely i would run next time for a
>> longer time 2-10 ns.
>> Here, I want to learn the a
OK, I started over with the CHCl3 box from scratch. I prepared the following
itp file from the CHCL3 parameters in ffG53a5.rtp:
---[chcl3.itp]---
[ moleculetype ]
; Namenrexcl
CHCL3 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass
1
ram bio wrote:
Dear Justin.
Thanks for the suggestion, definitely i would run next time for a
longer time 2-10 ns.
Here, I want to learn the analysis part of the mdrun, In order to
locate the lowest energy frame I executed command g_energy -f
md_0_1.edr -o PE.xvg and the output was
Statistic
Dear Justin.
Thanks for the suggestion, definitely i would run next time for a
longer time 2-10 ns.
Here, I want to learn the analysis part of the mdrun, In order to
locate the lowest energy frame I executed command g_energy -f
md_0_1.edr -o PE.xvg and the output was
Statistics over 51 steps
ram bio wrote:
Dear Justin,
Thanks for the suggestion and advice.
As i have used a modelled protein and want to obtain the lowest energy
configuration of the protein by doing dynamics, i want to collect the
structure (coordinates in pdb) representing average of all the
frames/configurations pr
There is a seq2itp.pl script provided by martini folks in their
website. You can get it from there.
Sunny
On Wed, Oct 21, 2009 at 9:42 AM, Francesco Pietra
wrote:
> Hi:
> I am looking for scripts that generate topology in coarse grained.
> Thanks for indications.
>
> francesco pietra
> _
Hi:
I am looking for scripts that generate topology in coarse grained.
Thanks for indications.
francesco pietra
___
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://ww
Dear Justin,
Thanks for the suggestion and advice.
As i have used a modelled protein and want to obtain the lowest energy
configuration of the protein by doing dynamics, i want to collect the
structure (coordinates in pdb) representing average of all the
frames/configurations produced in MD and al
Hi,
All TCL scripts dowloaded from the VMD website as well as mine are
supposed to be used within VMD. You have to run VMD first, then source the
script. Alternatively, you can source it in your .vmdrc file. After that,
you can run the g_cg function
Nicolas
>
>
>
>
>
>
>
> HI all,
>
leila karami wrote:
how can I do energy minimization with position restraint. how I creat
cooresponding mdp file? what should considered except what is seen in
below mdp file.
Reading the manual, wiki, and the many tutorials available will give you the
background you need. The obvious qu
leila karami wrote:
my pdb file for dna and protein contains 640 and 1130 atoms
respectively. if I want creat a new pdb file for studying pr-dna
interaction, should be numbering and order of numbers changed? how?
Numbering is the least of your worries, generating a reasonable starting
str
ram bio wrote:
Dear Mark,
Thanks for the advice and suggestions.
I have used trjconv command as in the justin tutorial (trjconv -s
md_0_1.tpr -f md_0_1.xtc -o md_0_1_noPBC.xtc -pbc mol -ur compact),
but when i loaded the md_0_1.gro followed by md_0_1_noPBC.xtc in VMD,
i could not see the prot
Apart from specifying -DPOSRES in your mdp file, you need to make sure that
posre.itp will be included into your topology. There is usually a statement
like 'ifdef POSRES ..."
Andreas
---
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On
Behalf
Baofu Qiao wrote:
HI all,
I have try the top2psf.tcl from Justin and the top2psf.pf from the VMD
website. But both of them can only deal with single chain system. Take
an example, if there are 10 proteins (+water) in my system, how to
convert to topology of the total system to .psf file? I
how can I do energy minimization with position restraint. how I creat
cooresponding mdp file? what should considered except what is seen in below
mdp file.
define= -DPOSRES
constraints = none
integrator = steep
nsteps = 100
emtol=
HI all,
I have try the top2psf.tcl from Justin and the top2psf.pf from the VMD
website. But both of them can only deal with single chain system. Take
an example, if there are 10 proteins (+water) in my system, how to
convert to topology of the total system to .psf file? I tried to append
the
my pdb file for dna and protein contains 640 and 1130 atoms respectively. if
I want creat a new pdb file for studying pr-dna interaction, should be
numbering and order of numbers changed? how?
___
gmx-users mailing listgmx-users@gromacs.org
http://lis
Dear Mark,
Thanks for the advice and suggestions.
I have used trjconv command as in the justin tutorial (trjconv -s
md_0_1.tpr -f md_0_1.xtc -o md_0_1_noPBC.xtc -pbc mol -ur compact),
but when i loaded the md_0_1.gro followed by md_0_1_noPBC.xtc in VMD,
i could not see the protein jumping out of
Hi Mark,
Thanks for your answer.
Mark Abraham ha scritto:
> There's nothing directional about the physics of a hydrogen bond, unless
> your model makes it so. There'd be nothing intrinsically valid or
> invalid with that either, so long as you parameterized the force field
> under that assumption
leila karami wrote:
dear Mark
thanks for your attention. is this mdp file true for energy minimization
(100 steps by steepest descent and 100 steps by/ conjugate gradient/)?
define= -DFLEX_SPC
constraints = none
*integrator = steep
nsteps = 1
ram bio wrote:
Dear Gromacs Users,
I have performed a protein in solvent simulation for 1 ns, the got the
output files as: md_0_1.cpt md_0_1.edr md_0_1.gro md_0_1.log
md_0_1.tpr md_0_1.trr md_0_1.xtc. I am following Justin Tutorial.
Can anybody tell me how to extract the coordinates ? of t
dear Mark
thanks for your attention. is this mdp file true for energy minimization
(100 steps by steepest descent and 100 steps by* conjugate gradient*)?
define= -DFLEX_SPC
constraints = none
*integrator = steep
nsteps = 100
integrator =
Nkwe Monama wrote:
Dear gmx-users,
I have been trying to run gromacs on IBM cluster on multiple nodes using
loadleveler script.
Do I have to compile gromacs on individual nodes? What do I have to do to run
it on multiple nodes?
That will depend how what your cluster is and how it is set up t
Dear Gromacs Users,
I have performed a protein in solvent simulation for 1 ns, the got the
output files as: md_0_1.cpt md_0_1.edr md_0_1.gro md_0_1.log
md_0_1.tpr md_0_1.trr md_0_1.xtc. I am following Justin Tutorial.
Can anybody tell me how to extract the coordinates ? of the simulated
prot
I tried to restart simulation, going back, from the time point where there was
no substantial change in the dimensions of the box, but simulations aborts again
after some time with the same error. The time points at which simulation aborts
are random. Having simulated for 25ns now i do not want t
leila karami wrote:
Hi
I want to creat mdp file for energy minimization (em.mdp). if I want to
minimize my system (pr+dna), by steepest descent and conjugate gradient
such as for example 100 steps by steepest descent and 100 steps by
conjugate gradient, how I can creat mdp file?
For exampl
my pdb file for dna and protein contains 640 and 1130 atoms respectively. if
I want creat a new pdb file for studying pr-dna interaction, should be
numbering and order of numbers changed? how?
___
gmx-users mailing listgmx-users@gromacs.org
http://lis
Hi
I want to creat mdp file for energy minimization (em.mdp). if I want to
minimize my system (pr+dna), by steepest descent and conjugate gradient such
as for example 100 steps by steepest descent and 100 steps by conjugate
gradient, how I can creat mdp file?
_
Hi Paer,
Thank you very much for your mail.
Here is the paper from where we are taking the MTSSL parameters
J. Phys. Chem. B 2008 112, 5755-5767, by B. Roux
and the supplementary in it.
Thank you.
Sudip
Pär Bjelkmar wrote:
Hi,
21 okt 2009 kl. 10.59 skrev Sudip Roy:
Thank you very much
---
>
> Message: 4
> Date: Wed, 21 Oct 2009 10:31:49 +0800
> From: wuxiao
> Subject: [gmx-users] Fatal error: 2 particles communicated to PME node
> 0 are more than a cell length out of the domain decomposition cell of
> their charge group
> To:
> Message-ID:
>
> Justin A. Lemkul wrote:
>>
>> I have also added a Perl script to the GROMACS site (the VMD page):
>>
>> http://www.gromacs.org/Developer_Zone/Programming_Guide/VMD
>>
>> The user provides an input topology file, and a .psf file is written,
>> which can be loaded as data for the structure in VMD.
Hi Omer,
Thanks for your input.
Let me reformulate my problem:
I have glycine molecules in the form of zwitterions:
1ZGLY N1 0.560 0.337 0.388 -0.0759 -0.2488 -0.5471
1ZGLYH12 0.625 0.312 0.461 0.6035 0.5922 -0.4315
1ZGLYH23
Hi Prem,
There is just something terribly wrong with your system if it goes
flat like that. But with only the information you give here, no one
can tell you more than that.
Cheers,
Tsjerk
On Wed, Oct 21, 2009 at 10:18 AM, Prem Singh Kaushal
wrote:
> Dear All
>
> I am using GROMCS 3.3.1 ver
their charge group
I utilized the GROMACS-4.0.5. I have searched the maillist to find some
similar posts but they can not yet cope with this issues. Could you give me
some clues, please?
Best wishes,
Chaofu Wu, Dr.
___
Dear Paer,
Thank you very much for your reply.
MTSSL is not a peptide, but it was parameterized by some
other group and we are trying to use the parameters. They have
used CMAP for MTSSL. So we also want to
take into account the CMAP in our gromacs calculations.
I am not much familiar with git
Dear All
I am using GROMCS 3.3.1 version. I had started the simulation of protein in
water with an octahedral box of dimension 9.76276 9.20449 7.97128 0.0
0.0 3.25425 0.0 -3.25425 4.60225. However after 25ns the
simulation aborts with the following error:
Fatal erro
On Wed, Oct 21, 2009 at 07:28, Enemark Soeren wrote:
> Dear users,
>
> I would like to compare interactions between molecules by using RDF. I have
> tried looking at glycine and water, and compare the following two
> interactions:
>
> 1) between the amine hydrogen atoms in glycine and the o
Dear gmx-users,
I have been trying to run gromacs on IBM cluster on multiple nodes using
loadleveler script.
Do I have to compile gromacs on individual nodes? What do I have to do to run
it on multiple nodes?
I get the following error message:
llsetpenv: execve failed with rc=-1 and errno=2
10
naimah haron naimah wrote:
Hello all
Did anyone know how to
1) calculate g_sdf?
Start with g_sdf -h.
2) ionic conductivity?
Don't know. Look in manual 7.4, 8 and maybe Appendix D.
Can I have the commands for that
If you do some more of your own work and ask focussed questio
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