smriti Sebastian wrote:
hi all,
I am new to GROMACS.I would like to know how we will simulate putting
more than two or more molecules of same proteins inside the box and do
simulation?Is there any possibility to replace 100 atoms or so of
solvent with proteins?
Please help.
You received
bh...@udsu.ru wrote:
Dear users.
Help me.
What parametres of force field OPLS it is necessary to be used
for group -N=CH2 (imine group) ?
Check out the OPLS papers for suitable groups or atom types that are present,
and if there's nothing already there, then you'll have to parameterize the
Hi all,
I used genconf because I wanted to replicate a membrane with ion channel
on the xy plane:
genconf -f conf.gro -o out.gro -nbox 2 2 1
Then I edited by hand the .top file where I modified the number of
molecules in the system.
When attempting to run, disregarding the number of processo
Fabio Affinito wrote:
Hi all,
I used genconf because I wanted to replicate a membrane with ion channel
on the xy plane:
genconf -f conf.gro -o out.gro -nbox 2 2 1
Then I edited by hand the .top file where I modified the number of
molecules in the system.
When attempting to run, disregardi
On 07/26/2011 04:19 PM, Justin A. Lemkul wrote:
Were the molecules whole in the coordinate file you replicated? If not,
the bonds will now be assigned across the entire box.
-Justin
Yes and not, depending on what you mean by "whole".
It is an ion channel, so it's made of four chains.
This cl
Fabio Affinito wrote:
On 07/26/2011 04:19 PM, Justin A. Lemkul wrote:
Were the molecules whole in the coordinate file you replicated? If not,
the bonds will now be assigned across the entire box.
-Justin
Yes and not, depending on what you mean by "whole".
It is an ion channel, so it's mad
On 07/26/2011 04:30 PM, Justin A. Lemkul wrote:
Fabio Affinito wrote:
On 07/26/2011 04:19 PM, Justin A. Lemkul wrote:
Were the molecules whole in the coordinate file you replicated? If not,
the bonds will now be assigned across the entire box.
-Justin
Yes and not, depending on what you m
Fabio Affinito wrote:
On 07/26/2011 04:30 PM, Justin A. Lemkul wrote:
Fabio Affinito wrote:
On 07/26/2011 04:19 PM, Justin A. Lemkul wrote:
Were the molecules whole in the coordinate file you replicated? If not,
the bonds will now be assigned across the entire box.
-Justin
Yes and not
Maybe this is a different issue... but it's ok that after the 99,999th
atom the counter restarts from zero?
21374SOL OW9 12.986 9.021 7.036 -0.0037 -0.4345 0.3977
21374SOLHW10 13.069 8.987 7.081 0.5916 0.5409 0.0638
Could this be the origin of my problem?
Than
Fabio Affinito wrote:
Maybe this is a different issue... but it's ok that after the 99,999th
atom the counter restarts from zero?
21374SOL OW9 12.986 9.021 7.036 -0.0037 -0.4345 0.3977
21374SOLHW10 13.069 8.987 7.081 0.5916 0.5409 0.0638
Could this be the or
On 07/26/2011 05:06 PM, Justin A. Lemkul wrote:
Fabio Affinito wrote:
Maybe this is a different issue... but it's ok that after the 99,999th
atom the counter restarts from zero?
21374SOL OW9 12.986 9.021 7.036 -0.0037 -0.4345 0.3977
21374SOL HW1 0 13.069 8.987 7.081 0.5916 0.5409 0.0638
Gmx-users,
There has been a earlier post on differences in entropies computed using the
covariance analysis and normal mode analysis
(http://lists.gromacs.org/pipermail/gmx-users/2009-April/041535.html). I
discovered the reason for the differences and thought that this information
might be use
Hi all
I used the genion to add a concentration and to neutalize the system in the
same time by using the
*genion -s file.tpr -conc 0.2 -neutral -o file.gro -random
so it did add the NA and Cl but it did not neutralize the system,
the net charge of the system still the same negative.
s
Dear all,
Is there a "trick" to get the numbers for g_covar -xmpa?
If not how can i calculate -xmpa results from -xpm -ascii results?
Thanks
Nihal
--
Elif Nihal Korkmaz
Research Assistant
University of Wisconsin - Biophysics
Member of Qiang Cui & Thomas Record Labs
1101 University Ave, Rm. 835
Fabio Affinito wrote:
On 07/26/2011 05:06 PM, Justin A. Lemkul wrote:
Fabio Affinito wrote:
Maybe this is a different issue... but it's ok that after the 99,999th
atom the counter restarts from zero?
21374SOL OW9 12.986 9.021 7.036 -0.0037 -0.4345 0.3977
21374SOL HW1 0 13.069 8.987 7.
Sara baretller wrote:
Hi all
I used the genion to add a concentration and to neutalize the system in
the same time by using the
*genion -s file.tpr -conc 0.2 -neutral -o file.gro -random
so it did add the NA and Cl but it did not neutralize the system, the net
charge of the
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PhD-position at the Institute for Physical and Theoretical Chemistry (IPTC) at
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We are seeking a highly motivated candidate for a PhD-position in the field of
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Im sorry for the confusion.
I used an .itp file from the UCalgary site for dpc, I input a line
[ molecules ]
; molecule name nr.
DPC 65
SOL 6305
in the dpc.top file.
However, I generated the .gro file directly from the m65.pdb file from the
UCalgary site using the editconf command.
>> WARNING 1
Hi All
I used the genion command using like this "genion -s file.tpr -conc 0.2
-neutral -o file.gro -random " again and i checked the md.log file and it
says that the net charge is negative like it was before using the genion
command.
so can anybody tell me what is wrong with the line genion -s
Janowicz, Adrianna C. wrote:
Im sorry for the confusion.
I used an .itp file from the UCalgary site for dpc, I input a line
[ molecules ]
; molecule name nr.
DPC 65
SOL 6305
in the dpc.top file.
However, I generated the .gro file directly from the m65.pdb file from the
UCalgary site using th
Sara baretller wrote:
Hi All
I used the genion command using like this "genion -s file.tpr -conc 0.2
-neutral -o file.gro -random " again and i checked the md.log file and
it says that the net charge is negative like it was before using the
genion command.
so can anybody tell me what is
Hi
this a part of the md.log where the system has -50 charge
two-body bonded interactions: 0.407 nm, Bond, atoms 514 515
multi-body bonded interactions: 0.731 nm, G96Angle, atoms 1272 1275
Minimum cell size due to bonded interactions: 0.804 nm
Maximum distance for 9 constraints, at 120 deg.
Sara baretller wrote:
Hi
this a part of the md.log where the system has -50 charge
two-body bonded interactions: 0.407 nm, Bond, atoms 514 515
multi-body bonded interactions: 0.731 nm, G96Angle, atoms 1272 1275
Minimum cell size due to bonded interactions: 0.804 nm
Maximum distance for 9
thanks! one last problem:
Im using the dpc.itp file & I keep getting an error having a problem with
the 0 mass for the atoms 11-23 (I've searched forums & haven't found
anyone having a problem with the 0 masses), along with No default Proper
Dih. types, No default Bond types No default Ryckaer
Janowicz, Adrianna C. wrote:
thanks! one last problem:
Im using the dpc.itp file & I keep getting an error having a problem with
the 0 mass for the atoms 11-23 (I've searched forums & haven't found
anyone having a problem with the 0 masses), along with No default Proper
Dih. types, No defaul
Hi Guys,
I met a problem when I ran qmmm using semi-empirical method in gmx,
"Subscript out of range on file line 659, procedure moldat.
Attempt to access the 0-th element of variable eheat.
Aborted"
I googled it, but there seems no archived info online. Has anyone met this
before?
Thanks,
thanks but i want to neutralize the system , why genion -s file.tpr -conc
0.2 -neutral -o file.gro -random does not neutralize the system to 0 .
On Tue, Jul 26, 2011 at 3:48 PM, Justin A. Lemkul wrote:
>
>
> Sara baretller wrote:
>
>> Hi
>>
>> this a part of the md.log where the system has -5
You are not specifying the ions to be added using the -pname and -nname options
with the genion command.
Perhaps that is a problem?
Warren Gallin
On 2011-07-26, at 2:49 PM, Sara baretller wrote:
> thanks but i want to neutralize the system , why genion -s file.tpr -conc 0.2
> -neutral -o file
Hello everyone,
I'm trying to run Gromacs, and use CPMD for QM. I have cpmd compiled and
running, but when I try to start mdrun_d with gromacs, I get the following
error:
QM/MM calculation requested.
Layer 0
nr of QM atoms 2
QMlevel: DIRECT/STO-3G
number of CPUs for gaussian = 1
memory for gauss
Warren Gallin wrote:
You are not specifying the ions to be added using the -pname and -nname options
with the genion command.
Perhaps that is a problem?
They are not necessary; the default names are used and should be correct for all
force fields now that naming has been standardized.
T
Hey Jacob,
I think you also have to use the flag --without-qmmm-gaussian.
Cheers,
Micha
On 26 Jul 2011, at 21:26, Jacob Jantzi wrote:
> Hello everyone,
>
> I'm trying to run Gromacs, and use CPMD for QM. I have cpmd compiled and
> running, but when I try to start mdrun_d with gromacs, I get th
Hello,
I am quite confused on whether it is better to use a standard cut-off
scheme for vdW interactions or if its better to use a switch or shift
function for this. I am doing a free energy calculation on the
solvation of a drug molecule in a solvent (on CHARMM ff) so I want to
be as accurate as
hi all
yes the gro file does have all ions, NA + number of ions equal to CL
number. so when i use grep command , i have same number of NA and CL and
that what tells me that something is wrong , because i should have another
50 ions of NA extra to neutralize the system
Thank you
On Tue, Jul
Fabian Casteblanco wrote:
Hello,
I am quite confused on whether it is better to use a standard cut-off
scheme for vdW interactions or if its better to use a switch or shift
function for this. I am doing a free energy calculation on the
solvation of a drug molecule in a solvent (on CHARMM ff)
Dear gmx-users,
I wish to calculate the number of solvent molecules within certain radius of
the protein all through the trajectory.
Is there any utility available with gromacs to do so?
Thanks,
SN
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-
Sara baretller wrote:
hi all
yes the gro file does have all ions, NA + number of ions equal to CL
number. so when i use grep command , i have same number of NA and CL and
that what tells me that something is wrong , because i should have
another 50 ions of NA extra to neutralize the syst
shivangi nangia wrote:
Dear gmx-users,
I wish to calculate the number of solvent molecules within certain
radius of the protein all through the trajectory.
Is there any utility available with gromacs to do so?
Dynamic selections can be made with g_select.
-Justin
--
===
Hari Shankar M wrote:
Gmx-users,
There has been a earlier post on differences in entropies computed using
the covariance analysis and normal mode analysis
(http://lists.gromacs.org/pipermail/gmx-users/2009-April/041535.html). I
discovered the reason for the differences and thought that this
Hi,
Where can I find the documentation for g_select?
Thanks,
SN
On Tue, Jul 26, 2011 at 6:07 PM, Justin A. Lemkul wrote:
>
>
> shivangi nangia wrote:
>
>> Dear gmx-users,
>>
>> I wish to calculate the number of solvent molecules within certain radius
>> of the protein all through the traject
Dear Gromacsers,
This seems more suited to gmx-developers but as the original thread was on
gmx-users, I'm posting it here.
Anyway, regarding the excessive memory usage of g_msd when using the -mol
flag, as reported recently, I believe I've identified the source of the
problem: the array of per-m
shivangi nangia wrote:
Hi,
Where can I find the documentation for g_select?
Manual section 8.1.2 or g_select -h. For specific usage examples search the
list archive (there are a number of posts on related topics) or:
g_select -select "help all"
-Justin
Thanks,
SN
On Tue, Jul 26, 2
You may have wanted to have sent the message to the gmx list!
XAvier.
Begin forwarded message:
From: nicoletta liguori
Date: July 26, 2011 5:28:29 PM MDT (CA)
To: x.peri...@rug.nl
Subject: density error bars
Hi,
I'm using Gromacs and its tools to sample some kind of membranes and
characte
Dear Friends
Does any of you know where can I obtain a FF for simulation of CNT and
Lonsdaleite solvated in water, that also contain parameters for N, H, O, P, Cl
and F.
Thanks
John Michael Espinosa-Duran
Electronics Engineer. M.Eng.
Universidad del Valle.
Cali, Colombia, South America.
Dear all:
I am working on a research to study whether the Lateral pressure
profile influence the protein function.
To get different lateral pressure profile, I used Parinello-Rahman
P coupling method and anisotropic pressure coupling with different p_ref
values(such as 0.9
KONG Xian wrote:
Dear all:
I am working on a research to study whether the Lateral
pressure profile influence the protein function.
To get different lateral pressure profile, I used
Parinello-Rahman P coupling method and anisotropic pressure coupling
with different
Hi Guys,
I met a problem when I ran qmmm using semi-empirical method in gmx,
"Subscript out of range on file line 659, procedure moldat.
Attempt to access the 0-th element of variable eheat.
Aborted"
I googled it, but there seems no archived info online. Has anyone met this
before?
Than
Dear Justin A. Lemkul:
Thanks for your rapid reply.
Just as you said, the result of my simulation with different xy
p_ref values didn't vary, they are almost the same.
I think I need consider some other ways to do what I was mean to
do.
I have read a paper
hint on how to do it.
Thank you
KONG Xian
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--
gmx-users mailing listgmx-users@gromacs.org
http
Greetings all,
I am quite interested in this discussion, and wondered if some people would
like to add how they would assess the length their MD simulations. I am
currently simulating HIV-1 RT for 1 ns and seem to have very flat energy
profiles for almost anything (energy wise) I care to measure
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