Thanks Justin. I have very recently started doing MD, guided by Gromacs
tutorials; not aware of this issue. Thanks for you suggestion, I will try with
Amber ff.
Sucharita Dey,PhD, Research Fellow, Cancer Science Institute of Singapore,
National University of Singapore. 14, Medical Drive, #12-0
On 3/17/14, 7:05 PM, dan42 wrote:
I am new to GROMACS. I am trying to use pdb2gmx to create a topology for PEG
(O-C-C)n with only H on one terminal and OH on the other. I know that I need
to add a residue entry to the forcefield for example to aminoacids.rtp in
Well, multiple residues actuall
I am new to GROMACS. I am trying to use pdb2gmx to create a topology for PEG
(O-C-C)n with only H on one terminal and OH on the other. I know that I need
to add a residue entry to the forcefield for example to aminoacids.rtp in
the gromos54a7.ff folder. However, I do not know how to construct the
On 3/17/14, 6:45 PM, Andrew DeYoung wrote:
Hi Tsjerk,
Thanks so much for your time. Unfortunately, when I tried to convert a .g96
configuration to a .trr trajectory, with this command:
trjconv -f conf1.g96 -o conf1.trr
I get this error message:
-
Hi Tsjerk,
Thanks so much for your time. Unfortunately, when I tried to convert a .g96
configuration to a .trr trajectory, with this command:
trjconv -f conf1.g96 -o conf1.trr
I get this error message:
---
Program trjconv_d, VERSION 4.5.5
Sou
Hi Andrew,
You can convert each frame to trr and concatenate those.
Cheers,
Tsjerk
On Mar 17, 2014 8:18 PM, "Andrew DeYoung" wrote:
> Hi,
>
> I have been creating several .g96 configuration files "by hand" (actually,
> using a scripting language).
>
> I like .g96 as a configuration file format
Hi,
I have been creating several .g96 configuration files "by hand" (actually,
using a scripting language).
I like .g96 as a configuration file format because it provides 9 decimal
places of precision for the x, y, and z coordinates of the position and
velocity of atoms in my system -- whereas
Dear Colleagues,
the next minor release is out now:
** CELLmicrocosmos 2.2.2_1 MembraneEditor Minor Release **
*Molecule Alignment and Performance Update, Bugfixes (17.03.2014)*
Shortly, here the number of improvements and bug fixes:
- All users of Linux distributions usind IcedTea for Java W
Dear Board,
I have done this with a steered MD, using covarience, etc...in the end there are nice delG and H,S line graphs...the only argument I have heard however is when doing the subtraction the third curve always gives the correct repective energy change, but the delG line graph may not
three questions regarding free energy calculations ...
1) i try running a free energy calculation and get an error msg:
"The Verlet cut-off scheme does not (yet) support free-energy calculations
with perturbed atoms, only perturbed interactions. This will be implemented
soon. Use the group schem
On 3/17/14, 10:52 AM, leila karami wrote:
Dear gromacs users
I will use pull = constraint (constraint pulling) for PMF calculations.
There is a tutorial about PMF from Justin in which he used
pull = umbrella (umbrella sampling).
In justin tutorial, step are as follows:
1) preparation of sys
Dear gromacs users
I will use pull = constraint (constraint pulling) for PMF calculations.
There is a tutorial about PMF from Justin in which he used
pull = umbrella (umbrella sampling).
In justin tutorial, step are as follows:
1) preparation of system
2) minimization & equilibration
3) gener
That kind of information is in the link I gave.
Mark
On Mon, Mar 17, 2014 at 7:22 AM, Chetan Mahajan wrote:
> Hi Mark,
>
> Could you clarify what is meant by "gentle" and why does it help solve the
> issue?
>
> Thanks
> Chetan
>
>
> On Sun, Mar 16, 2014 at 8:29 AM, Mark Abraham >wrote:
>
> > J
Hi! Thank you for reply.
You have lost me there, tbh.
I think I didn't make it clear, I have either organic -vely changed molecule
or Cl-. Those counterbalance the +vely charged material. Therefore, I either
have organics or clorine. So, if I do TI and completely decouple vow and
charges:
couple
Dear Roland, many thanks for that advice! I cloned the git repo (as of commit
b4619a45f3643c963c30b295eeec580882dd915a) and all my use cases are compiling
perfectly now. I still have to test how they actually work, but I'm
definitely a step forward in the right direction.
--
View this message in c
Hi
we have fixed quite a few installation issues since beta2. Could you try to
download the latest version from git?
git clone git://git.gromacs.org/gromacs.git
Let us know if you still see the issue.
If you don't have git you can download it from:
https://github.com/gromacs/gromacs/archive/mast
Hello everyone, my name is Jacek and I am new to GROMACS :) I have recently
downloaded and tried to compile the second beta of GROMACS 5, and run into
some issues along the way, so I decided to ask around and see if I can find
some help. Basically, what I wanted to do was to compile a few different
On 3/16/14, 11:35 PM, Sucharita Dey wrote:
Hello,
Thanks Justin.
Since my protein has a modified DNA residue (methyl cytosine) I have copied the "gromos53a6.ff" folder as well as the
"residuetypes.dat" file in my working directory and modified them, where I have inserted my modified DNA residu
Dear Gromacs users!
I've performed md simulation of water soluble protein having
water-assessable channel in its interior. I'd like to perform analysis
of average number of water molecules detected within the protein
interior during MD trajectory with the possible visualization of such
internal wa
I am a bit perplexed at this data about the box vector error I mentioned in
first email:
nstxout 1000 10 1 10 1000 1000 1000 1 nstvout 1000 10 1 10 1000 1000 1000
1 nstlog 1000 10 1 10 1000 1000 1000 1 nstenergy 1000 10 1 10 1000 1000
1000 10 nstxtcout 1000 10 1 10 1000 1000 1000 1 nstlist
On 2014-03-17 09:09, Andrew Bostick wrote:
Dear Justin
Very thanks for your guidance.
You are right. Excuse me for my several questions. I am beginner in
gromacs.
If I want to calculate delta H IN potein-ions interaction, can I use
g_energy?
Is Enthalpy by g_energy exact?
Is there a more app
On 2014-03-16 19:05, Andrew Bostick wrote:
Dear Justin
Thanks for your answer.
All of methods you mentioned ( PMF, TI, FEP, BAR) are used for calculating
free energy (G). In addition to free energy (G), I want to calculate
enthalpy (H) and entropy (S).
Are you sure can I use above methods for
Hi,
i want to calculate rmsd between residue.i searched before posted my query
but there is all about rmsf that i know how to calculate. kindly anyone
tell me how do i approach this problem.
--
With best regards,
SIDRA RAFI,
Jr.Research Fellow,P-103
Email: sidraraf...@gmail.com, sidra.r...@ic
Dear Justin
Very thanks for your guidance.
You are right. Excuse me for my several questions. I am beginner in
gromacs.
If I want to calculate delta H IN potein-ions interaction, can I use
g_energy?
Is Enthalpy by g_energy exact?
Is there a more appropriate tool for calculating delta H in grom
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