Hi GROMACS users,
I solved my proteinin a defined box of water. Now I want to add ions to
neutralize thesystem. But when I use “grompp -f ions.mdp -c solv.gro
-pgromacs.top -o ions.tpr” to generate the .tpr file I receive thiserror :
Fatal error:No such moleculetypeSOLFor more informationand
Thank you very much Justin for your helpful answer.
On Thursday, March 31, 2016 3:40 PM, Justin Lemkul <jalem...@vt.edu> wrote:
On 3/31/16 12:19 AM, mohammad r wrote:
> Thank you Justin, I want to do QM calculationbefore running equilibration
> then run the MD simulation by
AM, Justin Lemkul <jalem...@vt.edu> wrote:
On 3/30/16 2:17 AM, mohammad r wrote:
> Hi gromacs users,
>
>
>
> I want to do QMcalculation to my system. Can the PRODRG sitedo it (according
> to gromacs tutorial)? Or I should do it by using gromacsitself? By
Hi gromacs users,
I want to do QMcalculation to my system. Can the PRODRG sitedo it (according to
gromacs tutorial)? Or I should do it by using gromacsitself? By the way I’ve
generated the initial coordinate and topology files inamber tools then convert
it to gromacs format by using parmed
Thank you Justin for your help.
On Wednesday, March 9, 2016 6:38 PM, Justin Lemkul <jalem...@vt.edu> wrote:
On 3/9/16 1:42 AM, mohammad r wrote:
> Thank you Parham and Justin, Excuse me I have another question, in simulation
> of a water-peptide system, is it necessary
Lemkul <jalem...@vt.edu> wrote:
On 3/8/16 3:59 AM, mohammad r wrote:
> Thank you Parham
> You mean that it is not necessary to do QM/MM simulation?
>
The trivial task of adding ions to neutralize the net charge on the system
certainly does not require anything like
cation ::: Website :::
FaceBook
On Tue, Mar 8, 2016 at 3:32 PM, mohammad r <mohammad.r0...@yahoo.com> wrote:
Hi everybody, I’ve generated a water-peptide system, now I want to neutralize
it. Is adding adequate number of ions sufficient for neutralizing process or I
should do QM/M
Hi everybody, I’ve generated a water-peptide system, now I want to neutralize
it. Is adding adequate number of ions sufficient for neutralizing process or I
should do QM/MM simulation for the this process? Thank you, Mohammad.
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Hi GROMACS users,
I have some questions: 1- Can I model a carbonnanotube (CNT)
conveying fluid in GROMACS subjected to a magnetic field?2- How can I
check the centerof mass velocity of my system?3- I want to calculate
volumeand water self diffusion coefficient
Hi GROMACS users,
I have some questions:
1- Can I model a carbonnanotube (CNT) conveying fluid in GROMACS
subjected to a magnetic field?
2- How can I check the centerof mass velocity of my system?
3- I want to calculate volumeand water self diffusion
Thank you Justin,
do you know how I can find or modify the center of mass velocity of my system?
On Sunday, February 21, 2016 11:50 PM, Justin Lemkul <jalem...@vt.edu>
wrote:
On 2/21/16 3:15 PM, mohammad r wrote:
> Hi everybody,
>
>
>
> Is it correct to say the p
Hi everybody,
Is it correct to say the potential energy after energyminimization should be
negative and in the order of 105-106 ?according to gromacs tutorial:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/05_EM.html
Thank you, Mohammad.
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Gromacs Users
Thank you very much Justin
On Saturday, February 20, 2016 10:53 PM, Justin Lemkul <jalem...@vt.edu>
wrote:
On 2/20/16 8:49 AM, mohammad r wrote:
> Hi Justin,
>
> Thank you for your answer, I used grompp and it didn't give me error. I've
> attached a topology file
Hi gromacs users,
I've generatedinitial structure of my system by using ambertools (topology
andcoordinate files) and converted it to gromacs format (.gro and .top)by
parmed, but in topology file it doesn't refer to any forcefield.Does it make
any problem in the results or it is ok? Because
, 2016 6:31 PM, Justin Lemkul <jalem...@vt.edu> wrote:
On 2/15/16 1:31 AM, mohammad r wrote:
> I changed and reduced the ratio but the xpm file was not changed at all.
>
Unfortunately there's not much I can tell you here because this is rather
cryptic. It's illogical to get the
I changed and reduced the ratio but the xpm file was not changed at all.
On Sunday, February 14, 2016 5:05 PM, Justin Lemkul <jalem...@vt.edu> wrote:
On 2/14/16 1:54 AM, mohammad r wrote:
> Thank you Justin,
>
> I used xpm2ps command with below m2p file but
edu>
wrote:
On 2/13/16 1:33 AM, mohammad r wrote:
> Hi,
> I used the "gmx do_dssp" command to get the secondary structure of the
> protein during the simulation but the resolution of the resulted .xpm file is
> very low. how can I increase its resolution?
You can a
Hi,
I used the "gmx do_dssp" command to get the secondary structure of the protein
during the simulation but the resolution of the resulted .xpm file is very low.
how can I increase its resolution?
Thank you, Mohammad.
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Hi everybody,
I have the DMF pdb file and I want to import it to gromacs by pdb2gmx command,
but the residues are not included in none of the forcefields. can you please
help me figure this out?
Thank you, Mohammad.
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Hi everybody,
I want to convert the topology and coordinate files fromamber to gromacs
format. I used acpype bu it didn’t work properly (actually mysystem is
consisted of some lipids in a water-protein system but when I convertthe files
via acpype, the backbone is consisted of a mass
Hello everybody;
I want to install gromacs-5.0.5 in ubuntu-14.04 using the installation
instruction in the website "gromacs.org", but in the "cmake ..
-DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON" line I got this error:
-- No compatible CUDA toolkit found (v4.0+), disabling native GPU
Hi;
I tried to install GROMACS using "Installation guide for GROMACS 5.0.5" in the
gromacs.org, but I got an error after typing "cmake .. " line, then I tried
"sudo apt-get install gromacs" command, it installed the gromacs-4.6.5 but I
want the gromacs-5.0.5.
what should I do?
Thank you,
Hi everybody;
I have a cubic box with a peptide in its center (the .gro file). Now I want to
add some lipids (e.g. 3 molecules)(I have the .gro and .top and .pdb files of
the lipid) to this box. But I don't know how to do it.I think that "gmx
insert-molecules" command will help, but again I
Hi everybody;
I have a cubic box with a peptide in its center (the .gro file). Now I want to
add some lipids (e.g. 3 molecules)(I have the .gro and .top and .pdb files of
the lipid) to this box. But I don't know how to do it.I think that "gmx
insert-molecules" command will help, but again I
Hi;
I've used ff14sbamber force field to generate my system. As this force field
doesn'texist in gromacs, I generated the first structure of my system withamber
tools then I converted the topology and coordinate files intogromacs format by
using acpype. (In the amber tools I've added NaClto my
Hi;
I've alreadyconverted the amber topology and coordinate files to gromacs
format.But when I want to start running theenergy minimization first by using
the grompp to generate .tpr file,I get this error:
Program gmx, VERSION5.0.2Source code
Hi;
I've alreadyconverted the amber topology and coordinate files to gromacs
format.But when I want to start running theenergy minimization first by using
the grompp to generate .tpr file,I get this error:
Program gmx, VERSION5.0.2Source code
Hi;
I've alreadyconverted the amber topology and coordinate files to gromacs
format.But when I want to start running theenergy minimization first by using
the grompp to generate .tpr file,I get this error:
Program gmx, VERSION5.0.2Source code
Hi;I've alreadyconverted the amber topology and coordinate files to gromacs
format.But when I want to start running theenergy minimization first by using
the grompp to generate .tpr file,I get this error:
Program gmx, VERSION5.0.2Source code
Hi;
I've already converted topology and coordinate files which were generated with
amber tools to .gro format. But now, when I want to add 100Mm NaCl to the
system I get this error:
Fatal error:
No line with moleculetype 'SOL' found the [ molecules ] section of file
'c6m1_GMX.top'
For more
Hi;
I want to convert amber topology and coordinate files into gromacs topology
and coordinate file with the acpype command ( acpype -p FFF_AC.prmtop -x
FFF_AC.inpcrd ), but when I type it, I get this error: acpype: command not
found
I've done the procedure mentioned in the website:
Hi;
I want to use ff14SB Amberprotein force field. But it isn't included in the
gromacs force fields list.Is it possible to use this force field? How can I add
it in?Thank you, Mohammad.
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of the
present forcefields in gromacs.
Regards,-Maryam
On Sun, Aug 9, 2015 at 5:57 PM, mohammad r mohammad.r0...@yahoo.com wrote:
Hi;
I want to use ff14SB Amberprotein force field. But it isn't included in the
gromacs force fields list.Is it possible to use this force field? How can I add
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