Hi,
I am trying to run a vacuum simulation of a system associated with ATP and
peptide. Being vacuum MD i removed pressure coupling and included plain
electrostatic cut-offs while calculating potential. Energy minimisation
converged to machine precesion even though not upto the specified cut-of
nikhil damle wrote:
Hi,
I am trying to run a vacuum simulation of a system associated with ATP
and peptide. Being vacuum MD i removed pressure coupling and included
plain electrostatic cut-offs while calculating potential. Energy
minimisation converged to machine precesion even though not u
Hi,
It is a vacuum simulation. That's why a molecule can be considered in isolation
and i do not need to use periodic box. Secondly, even when i try to run the
process on 2 nodes it gives same error. So number of processors might not be
the actual reason.
Regards,
Nikhil
__
nikhil damle wrote:
Hi,
It is a vacuum simulation. That's why a molecule can be considered in
isolation and i do not need to use periodic box. Secondly, even when i
try to run the process on 2 nodes it gives same error. So number of
processors might not be the actual reason.
I still dis
Hi
can any one could help me in, How to include the pH for doing MD studies.
My interest is to include the pH at the initial time duration and to
change the pH from 4 to 7 during the course of simulation.
is there any possibility in performing such work in gromacs.
Thanks in advance
Parthiban
_
parthi...@ncbs.res.in wrote:
Hi
can any one could help me in, How to include the pH for doing MD studies.
My interest is to include the pH at the initial time duration and to
change the pH from 4 to 7 during the course of simulation.
is there any possibility in performing such work in gromacs
Thanks to Justin & Mark for answering my second question...
Could any one give me a hint on my first question that I copy it again?
--about g_velacc and calculating the diffusion constant from that. In
mailing list people say that we need to divide it by mass squared and 1/3.
Then I found another r
Dear Gmx users,
Does any one know why genbox stops when I use this command:
"genbox -cp resize.gro -cs spc216.gro -o b4em.pdb -p topol.top"
or when I use this command:
"genbox -cs spc216.gro -box 1 1 1 -maxsol 500 -o out.gro -p topol.top"
It goes until
Reading solvent configuration
Solvent configur
Jamie Seyed wrote:
Dear Gmx users,
Does any one know why genbox stops when I use this command:
"genbox -cp resize.gro -cs spc216.gro -o b4em.pdb -p topol.top"
or when I use this command:
"genbox -cs spc216.gro -box 1 1 1 -maxsol 500 -o out.gro -p topol.top"
It goes until
Reading solvent configu
Hi Justin,
yes resize.gro is a created file from editconf which has box size of
5.05918 on the last line
my command was "editconf -bt cubic -f spc216.pdb -o resize.gro -d 1"
and for second command I changed 1 to 5 but it still stops in the same
point. I am trying to examine 2 methods that you & Ma
Jamie Seyed wrote:
Hi Justin,
yes resize.gro is a created file from editconf which has box size of
5.05918 on the last line
my command was "editconf -bt cubic -f spc216.pdb -o resize.gro -d 1"
Do you actually have separate spc216.pdb and spc216.gro files? Just trying to
make sure this ac
I converted spc216.pdb to gro using editconf. SO they must be the same(?).
The version is 4.0.5 ...it was fine before... yes ran it just now for fws
tuto... how long it takes time in your machine?
On Sun, Oct 11, 2009 at 1:33 PM, Justin A. Lemkul wrote:
>
>
> Jamie Seyed wrote:
>
>> Hi Justin,
Jamie Seyed wrote:
I converted spc216.pdb to gro using editconf. SO they must be the
I suppose that's fine, I just don't see all the need for interconverting file
formats. It just opens up the possibility of more errors if you don't keep
track of what you're doing :)
same(?). The versio
Oh, I just changed the [-cs spc216.gro] to [-cp spc216.gro] and this is
working normally...??!! Do you have any idea?
On Sun, Oct 11, 2009 at 1:52 PM, Justin A. Lemkul wrote:
>
>
> Jamie Seyed wrote:
>
>> I converted spc216.pdb to gro using editconf. SO they must be the
>>
>
> I suppose that's
Jamie Seyed wrote:
Oh, I just changed the [-cs spc216.gro] to [-cp spc216.gro] and this is
working normally...??!! Do you have any idea?
Oops, I hadn't seen that before. That is what you should do. The -cp flag is
the coordinate file that should have solvent added to it, and that's what
On 11-10-2009 16:48, Justin A. Lemkul wrote:
parthi...@ncbs.res.in wrote:
Hi
can any one could help me in, How to include the pH for doing MD studies.
My interest is to include the pH at the initial time duration and to
change the pH from 4 to 7 during the course of simulation.
is there a
Jamie Seyed wrote:
Hi Justin,
But this seems that did not change the number of molecule in the output
(only the volume and density are changing) and it seems that -maxsol has
not been used... my full command
"genbox -cp spc216.gro -maxsol 500 -o out.gro -p topol.top -box 4 4 4"
if I change 5
Hi All,
I have added uploaded a new version of TopolGen, version 1.1, to the Users'
Contributions section of the website. This program is written in Perl and is
designed to generate a topology for use with the OPLS-AA force field from an
all-atom PDB file.
Based on input from many users of
Hi All,
I am working on the CG simulations of the proteins and lipid bilayers.
I am confused of how to set up the whole system for simulations. I got
the DSPC lipid bilayer from martini website and I have 1SU4.pdb file
with me. I cleaned the .pdb file and now I want to include the 14 DSPC
molecule
sunny mishra wrote:
Hi All,
I am working on the CG simulations of the proteins and lipid bilayers.
I am confused of how to set up the whole system for simulations. I got
the DSPC lipid bilayer from martini website and I have 1SU4.pdb file
with me. I cleaned the .pdb file and now I want to incl
Hi Justin,
Thanks for the quick reply. I am also following the martini tutorial
in order to do the CG simulations. Here are the following steps which
I am doing. Please have a look at them.
1) Cleaned the 1SU4.pdb file and renamed it to 1SU4_clean.pdb
2) converted 1SU4_clean.pdb to its CG structu
Hi Justin,
I have set up the whole system correctly but now at the final step
when I do mdrun it gives me the fatal error by saying that Number of
grid cells is zero. Probably the system and box collapsed.
Do you have any idea about this?
Sunny
On Sun, Oct 11, 2009 at 4:45 PM, sunny mishra w
sunny mishra wrote:
Hi Justin,
Thanks for the quick reply. I am also following the martini tutorial
in order to do the CG simulations. Here are the following steps which
I am doing. Please have a look at them.
1) Cleaned the 1SU4.pdb file and renamed it to 1SU4_clean.pdb
2) converted 1SU4_cle
sunny mishra wrote:
Hi Justin,
I have set up the whole system correctly but now at the final step
when I do mdrun it gives me the fatal error by saying that Number of
grid cells is zero. Probably the system and box collapsed.
Then "correctly" is debatable :)
Do you have any idea about thi
Hello,
How can we use the trr file in VMD? I thought since we ask in the mdp
file to output the velocities, then in VMD we should be able to see
molecules colored based on their velocities through the trajectory
options. Am I correct?
Payman
___
gmx-use
yes you can do that by opening the gro file and then loading the .trr file .
amit
On Sun, Oct 11, 2009 at 6:22 PM, Paymon Pirzadeh wrote:
> Hello,
> How can we use the trr file in VMD? I thought since we ask in the mdp
> file to output the velocities, then in VMD we should be able to see
> molec
I did that but, it did not work! I just get a constant color.
On Sun, 2009-10-11 at 18:27 -0700, Amit Choubey wrote:
> yes you can do that by opening the gro file and then loading the .trr
> file .
>
> amit
>
> On Sun, Oct 11, 2009 at 6:22 PM, Paymon Pirzadeh
> wrote:
> Hello,
>
Paymon Pirzadeh wrote:
I did that but, it did not work! I just get a constant color.
Unless the velocity is written to a field that VMD recognizes, I don't think
you'll be able to see the velocities colored. For example, VMD can color by
B-factor or occupancy, neither of which would be us
Paymon Pirzadeh wrote:
I did that but, it did not work! I just get a constant color.
At the very least you would need to choose a representation that would
colour by velocities. I don't know whether VMD can do that, or read .trr
velocities in the first place, however. You might be better serv
>
>Jinyao Wang wrote:
>> Hi gmx-users锛?
>>
>> I want to calculate the non-bond interaction (LJ+Coulomb) between solvent and
>> solvent in pure solvent system. After the simulation of my pure solvent
>> system, I calculated the interaction between solvent and solvent using the
>> rerun option of th
Justin A. Lemkul wrote:
Paymon Pirzadeh wrote:
I did that but, it did not work! I just get a constant color.
Unless the velocity is written to a field that VMD recognizes, I don't
think you'll be able to see the velocities colored. For example, VMD
can color by B-factor or occupancy, nei
Well,
I would like to have each molecule's velocity magnitude in each frame
(like an xtc file), and then watch it in VMD to see how different parts
of a system will evolve in terms of their kinetics. Then, I think using
the scale in the trajectory option of VMD, we might be able to see sth.
no?
Jinyao Wang wrote:
Jinyao Wang wrote:
Hi gmx-users锛?
I want to calculate the non-bond interaction (LJ+Coulomb) between solvent
and solvent in pure solvent system. After the simulation of my pure
solvent system, I calculated the interaction between solvent and solvent
using the rerun option of
Jinyao Wang wrote:
>> Jinyao Wang wrote:
>>> Hi gmx-users锛?
>>>
>>> I want to calculate the non-bond interaction (LJ+Coulomb) between solvent
>>> and
>>> solvent in pure solvent system. After the simulation of my pure solvent
>>> system, I calculated the interaction between solvent and solvent usi
Paymon Pirzadeh wrote:
Well,
I would like to have each molecule's velocity magnitude in each frame
(like an xtc file), and then watch it in VMD to see how different parts
of a system will evolve in terms of their kinetics. Then, I think using
the scale in the trajectory option of VMD, we might
>From: XAvier Periole
>Subject: Re: [gmx-users] how to calculate the non-bond interaction
> between solvent and solvent in pure solvent system
>To: Discussion list for GROMACS users
>Message-ID:
>Content-Type: text/plain; charset=GB2312; format=flowed; delsp=yes
>
>> I want to cal
Jinyao Wang wrote:
>
>> From: XAvier Periole
>> Subject: Re: [gmx-users] how to calculate the non-bond interaction
>> between solvent and solvent in pure solvent system
>> To: Discussion list for GROMACS users
>> Message-ID:
>> Content-Type: text/plain; charset=GB2312; format=flowed;
Jinyao Wang wrote:
From: XAvier Periole Subject: Re: [gmx-users] how to
calculate the non-bond interaction between solvent and solvent in pure
solvent system To: Discussion list for GROMACS users
Message-ID:
Content-Type: text/plain;
charset=GB2312; format=flowed; delsp=yes
I want t
>> Hi Justin, Thank you for your reply. But I still don't know how to set the
>> "energygrps" option in the rerun.mdp for calculating the interaction between
>> solvent molecule and solvent molecule in pure solvent system. As you said
>> that these terms should be obtained running the g_energy,coul
Jinyao Wang wrote:
Hi Justin, Thank you for your reply. But I still don't know how to set
the "energygrps" option in the rerun.mdp for calculating the interaction
between solvent molecule and solvent molecule in pure solvent system. As
you said that these terms should be obtained running the g_
Jinyao Wang wrote:
>>> Hi Justin, Thank you for your reply. But I still don't know how to set the
>>> "energygrps" option in the rerun.mdp for calculating the interaction between
>>> solvent molecule and solvent molecule in pure solvent system. As you said
>>> that these terms should be obtained ru
Hi gmx users,I am now simulating one protein with solvent, in all atom
forcefield, gromacs official distributed version. The pressure of system
seems to be unreasonable large, and during the whole process, the box keeps
increasing.
Here is how I set up the system,
1. I solvate the prote
Plot the fluctuations of the pressure with time for the simulation. Far
better way I think to get an idea of what is going on with a property
than just looking at values in a log file. Especially when you are
starting out.
With pressure coupling, it is not unusual to have a fluctuation of a
h
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