within the error bars even though I use different schemes for
ewald_geometry?
Regards
--
Ozge Engin- PhD candidate
Koc University, College of Engineering
Dept. of Computational Sciences & Engineering
Rumelifeneri
expect to get a number
other than 0 at the lower and upper boundaries. I have also searched the
mailing list. There was an e-mail similar to that one, but it was not
replied.
I have attached the density profile in the attachment.
Why is it the case?
Regards
--
Ozge Engin
dens.xvg
Description
depending on the block
size used and number of bootstraps. I could not find a way to calculate the
error for the umbrella sampling simulation by means of that output file.
Thanks in advance
--
Ozge Engin
Department of
nds are created successfully, but when I
looked at the screen I could see only one of those CG bonds, but not the
others. Why might be the reason?
Thanks in advance
--
Ozge Engin
★☆
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Please sear
ns in topology file seem not working for big
> systems (Berk Hess)
> 3. "coarse_grain.tcl" script does not show all of the
> coarse-grained bonds in vmd (Ozge Engin)
> 4. Re: "coarse_grain.tcl" script does not show all of the
> coarse-grained bon
peptide is not translated, but sitting at the center of the box. Why is
the case? Any suggestions?
Thanks in advance
--
Ozge Engin
★☆
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hat may be the problem?
Best Regards
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+03
What may be the problem?
Best Regards
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problems.
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★☆
genera_start_4
Description: Binary data
input
Description: Binary data
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> The run ended successfully:
> >
>
> >
>
> >
>
> >
> Then i used the command
> >
>
> >
> g_nmeig_d -f new_nm.mtx -s new_nm.tpr -ol eigenvalue.xvg -v eigenvector.trr
> >
>
> >
>
> >
>
> >
> I get the follow
Hi all,
Somebody has sent a mail which is about the address of a server in which the
temperatures for a REMD simulation is calculated. However, I can not find this
mail. Could you sent the address of the server, please?
Thank you
Ozge Engin
=
Computational
1.0 1.0 .70 .40 1.0
Replica exchange at step 47000 time 94
Line 2: Repl 2 <-> 3 dE = 7.473e-01
Repl ex 0 x 1234 x 56 x 78 x 9 10 11 12 13
Repl pr .04 .47 1.0 1.0 .65 .60 .34
Thanks in advanc
lman/listinfo/gmx-users
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Ozge Engin
===
Hi all,
What does the second column of the output file of g_cluster with -dist option
stand for? Its title is a.u. I think it is atomic unit? In the manual, it is
not described.
Thanks in advance
Ozge Engin
=
Computational Science & Engineering
Koc Univer
put of g_cluster with -dist
option
On Tue, 12 Feb 2008 23:55:35 +0200
"OZGE ENGIN" <[EMAIL PROTECTED]> wrote:
> Hi all,
>
> What does the second column of the output file of g_cluster with -dist
>option stand for? Its title is a.u. I think it is atomic unit? In the m
rmsd matrix?
Thanks in advance
Ozge Engin
=
Computational Science & Engineering
Koc University
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Please search
the total number of
conformations obtained from the simulation.
Thanks in advance
Ozge Engin
=
Computational Science & Engineering
Koc University
___
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http://www.gromacs
Date: Fri, 15 Feb 2008 09:11:55 +1100
Subject: Re: [gmx-users] still got the problem with the output of g_cluster
OZGE ENGIN wrote:
> Hi all,
>
> I have still got the problem with the second column of the output of
> g_cluster with -dist option. Xavier said that the a.u stands for arb
s the sum of the second column?
Mark
- Original Message -
From: OZGE ENGIN <[EMAIL PROTECTED]>
Date: Friday, February 15, 2008 9:46 am
Subject: Re: Re: [gmx-users] still got the problem with the output of g_cluster
To: gmx-users@gromacs.org
> Hi Mark,
>
> You are right
i.e. 3001*3000*0.5, which is the number you give below. The
values in this column are consistent with a histogram.
Mark
- Original Message -----
From: OZGE ENGIN <[EMAIL PROTECTED]>
Date: Friday, February 15, 2008 6:32 pm
Subject: Re: Re: Re: [gmx-users] still got the problem wi
RMS deviation. What is the difference between these two?
One of them gives the absolute rmsd of each frame and the other gives the
relative rmsd according to the average rmsd?
Thanks in advance
Ozge Engin
=
Computational Science & Engineering
Koc Univer
Hi all,
There are two options for the -dista option of the g_cluster: rmsd of distance
and RMS deviation.
What is the difference between these two?
One of them gives the absolute rmsd of each frame and the other gives the
relative rmsd according to the average rmsd?
Thank you
Ozge Engin
D]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Ozge Engin
=
Computational Science & Engineering
Koc University
___
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http://www.gromacs.org/mailman/l
t;other options" part for -dista option.
Maybe I could not understand. Could anyone explain this in a clearer way,
please?
Thanks in advance
Ozge Engin
=
Computational Science & Engineering
Koc University
___
g
me cut-off value, they are grouped in different clusters, Why?
Thank you.
-Original Message-
From: Mark Abraham <[EMAIL PROTECTED]>
To: Discussion list for GROMACS users
Date: Sun, 17 Feb 2008 22:35:20 +1100
Subject: Re: [gmx-users] distance options for g_cluster
OZGE ENGIN wrote:
parameters for dihedral angles.
Thanks in advance
Ozge Engin
=
Computational Science & Engineering
Koc University
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Please se
nks in advance
Ozge Engin
=
Computational Science & Engineering
Koc University
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Please search the archive
roblem with exchange probabilities in remd
OZGE ENGIN wrote:
> Hi all,
>
> I am performing a remd simulation of a peptide+water system. I have tried
> different temperature distributions. I am using an NVT ensemble. My
> temperature coupling constant is 0.1 ps.
>
> The proble
bond. What
additional steps do I follow to construct this bond ?
Thanks in advance
Ozge Engin
=
Computational Science & Engineering
Koc University
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chive at http://www.gromacs.org/search before posting!
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www interface or send it to [EMAIL PROTECTED]
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Ozge Engin
=
Computationa
numbers into these
columns.
P.S: I use Gromacs 3.3.1
Thanks in advance
Ozge Engin
=
Computational Science & Engineering
Koc University
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ot; and "no") .
How can I implement it to my system? I use Gromacs 3.3.1 version.
Thanks in advance
Ozge Engin
=
Computational Science & Engineering
Koc University
___
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the main (longer)
simulation. Consequently, I want to change the time step and use tpbconv to
restart.
Is there any way to do that?
Thanks in advance...
Ozge Engin
=
Computational Science & Engineering
Koc Univer
ubject: Re: [gmx-users] changing the time step with tpbconv
OZGE ENGIN wrote:
> Hi all,
>
> I am performing an 80-ns simulation. During the optimization of the
> parameters that were used in this run, I had performed some small test
> simulations, and used short frequency values to
, VERSION 3.3.1
Source code file: grompp.c, line: 542
Fatal error:
Can not start from an incomplete frame
Ozge Engin
=
Computational Science & Engineering
Koc University
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that, I will copy the ions definitions that were given in the
ffamber96.rtp file to the ions.itp file?
I am a little bit confused because the definition of ions in AMBER is
completely different from those of OPLS and GROMOS ff.
Thanks in advance
Ozge Engin
9 Mar 2008 11:54:22 -0400
Subject: Re: [gmx-users] transfer of AMBER ion definitions to the ions.itp file
Quoting OZGE ENGIN <[EMAIL PROTECTED]>:
> Hi all,
>
> I am trying to use AMBER96 ff under GROMACS package. I read the suggestions
> that were given at http://chemistry.csulb.
corresponding H names of this residue have been defined in .rtp and
.hdb,respectively.
So, what may be the problem?
Thanks in advance
Ozge Engin
=
Computational Science & Engineering
Koc University
___
gmx-u
+++
I looked at both the .rtp and .hdb files, but everything seems to be correct.
Does anybody face with a similar problem?
Thanks in advance
Ozge Engin
=
Computational Science & Engineering
Koc Univer
ce for the force on atoms.
-Original Message-
From: "Justin A. Lemkul" <[EMAIL PROTECTED]>
To: Discussion list for GROMACS users
Date: Mon, 31 Mar 2008 14:42:55 -0400
Subject: Re: [gmx-users] error with pdb2gmx when using AMBER ff in GROMACS
Quoting OZGE ENGIN <[EMAIL PRO
or GROMACS users
Date: Mon, 31 Mar 2008 15:25:11 -0400
Subject: Re: Re: [gmx-users] error with pdb2gmx when using AMBER ff in GROMACS
Quoting OZGE ENGIN <[EMAIL PROTECTED]>:
> I already indicated the problem that I have. If I put an N prefix to the
> first residue, I get warning of
again.
-Original Message-
From: "Justin A. Lemkul" <[EMAIL PROTECTED]>
To: Discussion list for GROMACS users
Date: Mon, 31 Mar 2008 17:41:50 -0400
Subject: Re: Re: Re: [gmx-users] error with pdb2gmx when using AMBER ff in
GROMACS
Quoting OZGE ENGIN <[EMAIL PROTECTED]
should give me that area?
Regards
--
Ozge Engin
★☆
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w
calculation?
Regards
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★☆
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sets.
I searched the internet to find a study regarding the concentration
dependency of the PMF.
Is this reasonable? Any suggestions?
Regards
Ozge Engin
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Please search the archive at http
-af3d-e6c88393d...@rug.nl>
> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
>
>
> On Jun 1, 2010, at 9:13 PM, Ozge Engin wrote:
>
> > Hi all,
> >
> > I am trying to calculate the potential of mean force between the two
> > hydr
the whole data to 4, and calculated the
standard deviation between the 4 sets, and divided the result by sqrt (3).
For the Xavier's suggestion: I think I should wait a little, at least until
having the same length of trajectory for the two sets.
Thanks
--
Ozge Engin
★☆
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what does "histogram of
configurations" mean?
Thank you
--
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★☆
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little
bit detailed information, please?
Thanks in advance
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★☆
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straightforward?
Regards
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:
Program grompp, VERSION 3.3.1
Source code file: toppush.c, line: 891
Fatal error:
moleculetype CU1+ is redefined
What is the problem?
Thanks in advance
Ozge Engin
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, what may be the problem?
Thanks in advance!
Ozge Engin
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Please don't
rotein 1
NA+ 12
SOL 1589
OZGE ENGIN a écrit :
> Hi all,
>
> I have a problem with position-restrained (pr) dynamics of a charged residue
> in a water box. Up to the position-restrained step, the method worked well;
> however, it gave the f
rotein 1
NA+ 12
SOL 1589
OZGE ENGIN a écrit :
> Hi all,
>
> I have a problem with position-restrained (pr) dynamics of a charged residue
> in a water box. Up to the position-restrained step, the method worked well;
> however, it gave the f
rained dynamics of a charged
system
Maybe you have forget to include something (I don't know exactly what)
...
is it possible to post your top and gro files (attached and zipped) ?
it will be easier to find what happened :P .
OZGE ENGIN a écrit :
> Yes, Sebastien! It ends as you wrote. So, it
rained dynamics of a charged
system
Maybe you have forget to include something (I don't know exactly what)
...
is it possible to post your top and gro files (attached and zipped) ?
it will be easier to find what happened :P .
OZGE ENGIN a écrit :
> Yes, Sebastien! It ends as you wrote. So, it
Dear gromacs-users,
I have a problem with the output file of g_density. It uses .tpr and .trr files
in order to make calculations. I have made the .trr file using the parameters
below. Since total step size is 100 and I have written the coordinates at
each 50 steps, I expect to have more th
the system?
Thanks in advance!
Ozge Engin
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Please don't post (un)subs
tween the oppositely charged residues :-) is not far
apart than the optimum which means that they are located at such a distance
that they have the ability to cancel each other.
Thank you...
Ozge Engin
-Original Message-
From: Mark Abraham <[EMAIL PROTECTED]>
To: Discussi
Hi,
I want to get the radial distribution of my system which is composed of a box
of capped alanine residues (CAR). In this respect, I used g_rdf command with
-com option. I chose one of the CAR s as the first, and the others as the
second group. In manual, for -com option, it is written that t
Hi gromacs-users,
I want to simulate a box of that is composed of capped (ACE and NME to N and C
termini, respectively) tryptophan molecules.
As a first stage, I minimized single capped trp molecule, and then used it with
genconf command along with the options -rot ans -nbox.
In this case, I
Hi all,
As you suggest David I used genconf command without -rot option. I minimized a
single capped trp molecule and got the minimized molecule and used that
molecule with genconf command in order to create a box.
>
> Then, I solvated capped trp molecule within the created box with genbox
> c
Hi all,
I want to measure the density or volume of the whole simulation box not only
the molecule. I could not find an appropriate command. I found some;however,
they measured the partial densities across the box.
Thanks in advance...
Ozge
___
gmx-u
Hi all,
I can not understand why it is required to take same values for both r_list
and r_coulomb parameters when using PME for calculation of electrostatic
interactions?
I read archieve, and gromacs manual. In archieve, similar question had been
posted, but not replied yet.
Thanks in advanc
ntion!
Oz.
-Original Message-
From: David van der Spoel <[EMAIL PROTECTED]>
To: Discussion list for GROMACS users
Date: Sat, 01 Sep 2007 13:37:05 +0200
Subject: Re: [gmx-users] r_list and r_coulomb values while using PME
OZGE ENGIN wrote:
> Hi all,
>
> I can not underst
ubject: Re: [gmx-users] r_list and r_coulomb values while using PME
OZGE ENGIN wrote:
> 'The force is not the derivative of the potential', is it due to the types of
> calculations performed in PME, using of FFT for reciprocal sum? Because it
> does not matter while using reacti
Hi all,
I have read the manual of Gromos force field with parameter set 53A6. I am
trying to get the topology file of cyclohexane molecule.
In a paper which defined the parameters of Gromos 53A5 and 53A6 force-fields,
it is said that atoms that are not listed have a zero charge, and the charge
Hi all,
Is there any tool for the visualization of disulphide bonds along the whole
trajectory?
Regards,
Ozge
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Hi Yang,
I am performing a simulation of a peptide in vacuum, and in the mailing
archieve, I read that using of linear option of comm_mode in the vacuum
simulations.
Is it due to the relatively rapid convergence of molecules in the vacuum
environment?
Thanks in advance
Ozge
-Original
visible.
Is it related to conservation of angular momentum?
Thank you very much!
Oz.
-Original Message-
From: Yang Ye <[EMAIL PROTECTED]>
To: gmx-users@gromacs.org
Date: Sun, 14 Oct 2007 07:07:18 -0700 (PDT)
Subject: Re: Re: [gmx-users] the comm_mode
- Original Message
Fro
Hi all,
I am simulating a charged peptide in vacuum. I want to neutralize my system by
using genion command,and as expected it asks me a continuous solvent group for
the replacement; however, I have no solvents.
How can I add ions to my system if I am in vacuum? or Is it necessary to add
ions
Hi Mark,
I think, it is not a chemistry question exactly.
Genion command asks for a group whose atoms are replaced with ions.
I have no solvent molecules in my system.
In this respect, how can I incorporate ions into my system?
Thanks
Ozge
-Original Message-
From: "Mark Abraham" <[EM
Hi all,
I am performing a simulation of an amphilic peptide at air/water interface. I
want to start to simulation in which the peptide is placed at the interface.
I changed the center of the system so that the center is now located at
interface. Then, I used editconf command with -c option in o
Hi all,
I am performing a simulation of an amphilic peptide at air/water interface. I
want to start to simulation in which the peptide is placed at the interface.
I changed the center of the system so that the center is now located at
interface. Then, I used editconf command with -c option in o
Hi Mark,
I am so sorry, but I erased your mail before reading it. So, could you please
send the mail one more time? It is important to me.
Thank you very much
Ozge
-Original Message-
From: "OZGE ENGIN" <[EMAIL PROTECTED]>
To: gmx-users@gromacs.org
Date: Sun, 04 Nov 200
Hi all,
I am performing a simulation of peptide at air/water interface.
The box vectors are: x,y,z where 2x=2y=z. After loading the trajectory to the
vmd, I realized that water molecules moved out of bulk water in the z
direction: into the vacuum. However, the peptide also moved out of the bulk
rforming simulation at air/water interface
Regarding the peptide moving out of the box, it is only a visualization
artifact.
Try trjconv -pbc inbox.
2007/11/5, OZGE ENGIN <[EMAIL PROTECTED]>:
>
> Hi all,
>
> I am performing a simulation of peptide at air/water interface.
>
&g
I want to use replica exchange method. After obtaining all files at different
temperatures, how can I load the e.g 4 separate replica files to the mdrun
command?
I could not find any information about it.
Thank you
Oz.
___
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Hi all,
I want to extract some frames from the whole trajectory. So, I used -trjconv
with (b) and (e) options.
P.S: I use the Gromacs 3.3.1 version.
But I got the following error:
Select a group: 0
Selected 0: 'System'
Last frame -1 time0.000
Precision of traj.xtc is 0.001 (nm)
W
Hi all,
I want to extract some frames from the whole trajectory. So, I used -trjconv
with (b) and (e) options.
P.S: I use the Gromacs 3.3.1 version.
But I got the following error:
Select a group: 0
Selected 0: 'System'
Last frame -1 time0.000
Precision of traj.xtc is 0.001 (nm)
W
t work
Dear Ozge,
What was the command line exactly?
Ran.
OZGE ENGIN wrote:
> Hi all,
>
> I want to extract some frames from the whole trajectory. So, I used -trjconv
> with (b) and (e) options.
>
> P.S: I use the Gromacs 3.3.1 version.
>
> But I got the following error:
&g
t work
Dear Ozge,
What was the command line exactly?
Ran.
OZGE ENGIN wrote:
> Hi all,
>
> I want to extract some frames from the whole trajectory. So, I used -trjconv
> with (b) and (e) options.
>
> P.S: I use the Gromacs 3.3.1 version.
>
> But I got the following error:
&g
n list for GROMACS users
Date: Mon, 19 Nov 2007 17:53:16 +0100
Subject: Re: [gmx-users] trjconv does not work
I see. Do you have any structure between t=0.1ps and t=0.2ps?
Ran.
OZGE ENGIN wrote:
> The command line ws the following:
>
> trjconv -s peptide_b4md.gro -f traj.xtc -b 0.1 -
option,
and -multi does not take an argument.
If you use the CVS head branch, you need to set -np and -multi
both with an argument.
Berk.
>From: "OZGE ENGIN" <[EMAIL PROTECTED]>
>Reply-To: Discussion list for GROMACS users
>To: gmx-users@gromacs.org
>Subject: Re: RE: [gmx-
Hi All,
I am performing replica exchange molecular dynamics simulation(REMD). I have 16
replicas each of which has a peptide with different conformation. After
obtaining .tpr files (at desired temperatures) for each replicas, I loaded them
via mdrun, but I got the following error:
Fatal error:
t;
To: gmx-users@gromacs.org
Date: Fri, 23 Nov 2007 10:36:57 +0100
Subject: RE: [gmx-users] problem with mdrun performing replica exchange MD
>From: "OZGE ENGIN" <[EMAIL PROTECTED]>
>Reply-To: Discussion list for GROMACS users
>To: gmx-users@gromacs.org
>Subject: [gmx-
e the CVS head branch, you need to set -np and -multi
both with an argument.
Berk.
>From: "OZGE ENGIN" <[EMAIL PROTECTED]>
>Reply-To: Discussion list for GROMACS users
>To: gmx-users@gromacs.org
>Subject: Re: RE: [gmx-users] problem with mdrun performing replica exch
Hi all,
I am performing a simulation in vacuum. The peptide has nonzero charge, so I
attempted to neutralize the total charge via genion;however as it is known, it
asks for a continuous group for replacing, but I have no solvent molecules for
the replacement.
How can I neutralize the total ch
Hi all,
I am performing a REMD simulation in vacuum. Although I minimized the energy of
each initial replica by using a stringent convergence criterion, after the the
third attempt, the system exploided because of a huge deviation in the Lincs
algorithm.
Although I started to the simulation vi
Hi all,
I am performing a REMD simulation in vacuum. Although I minimized the energy of
each initial replica by using a stringent convergence criterion, after the the
third attempt, the system exploided because of a huge deviation in the Lincs
algorithm.
Although I started to the simulation vi
Hi all,
I have a question about the output file of g_sas. The fifth column corresponds
to Solvation free energy.
I selected the whole peptide for analyzing. It did not take negative value, but
rather it took positive values.
As it takes larger + values, it means that the peptide or group under
Hi Monica,
I had not found a detailed tutorial about it; however, you can search for
papers in which the simulations are performed via REMD.This will be helpful.
Ozge.
-Original Message-
From: "Monika Sharma" <[EMAIL PROTECTED]>
To: gmx-users@gromacs.org
Date: Fri, 30 Nov 2007 17:04:07
Hi,
I have a problem with g_hbond. I want to investigate the H bonds formed not
only within the protein but also between water molecules and the protein.In
this respect, I select the group 0 --> 'system' option for both selections, an
error message like the following one appears:
Segmentation
Message-
From: Erik Marklund <[EMAIL PROTECTED]>
To: Discussion list for GROMACS users
Date: Mon, 18 Dec 2006 13:48:18 +0100
Subject: Re: [gmx-users] g_hbond
On Mon, 2006-12-18 at 13:34 +0200, OZGE ENGIN wrote:
> Hi,
>
> I have a problem with g_hbond. I want to investigate the
Hi,
I have some questions about g_hbond option.
1) My system consists of a protein molecule (a capped 1 alanine residue)
(CH3-CO-ALA-NH-CH3) and 250 water molecules. After selecting the g_hbond
option, it says that protein molecule consists of 12 elements; however, it
consists much more el
Hi,
First of all, thank you very much for your earlier explanations, they helped me
much. Now, I have a problem with the -sel option of g_hbond. I want to
analyze the specific hydrogen bonds in my system, in this respect I created a
file (.ndx), and then I called it with the -sel option. The
Hi,
I have a problem with the -hbn option. I could not understand the output
given. It is indicated that there is only one type of hydrogen bond is formed
between the donor and acceptor (Only one triplet is given). It means that the
same hydrogen bond is formed between the same atoms during th
Hi,
By using the hnum option of g_hbond, I was able to get the hbond.ndx file.
However, I want to know exactly which atom groups take participate to the
formation of that hbonds over each frame both for prot-prot and prot-solvent.
How can I do that? (In hbond.ndx file, as you know, the hbonds
Hi,
By using the hnum option of g_hbond, I was able to get the hbond.ndx file.
However, I want to know exactly which atom groups take participate to the
formation of that hbonds over each frame both for prot-prot and prot-solvent.
How can I do that? (In hbond.ndx file, as you know, the hbonds a
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