Hi everybody
I want to build a simulation box fill of water and some SDS molecules. To
do this at first I fill the box with SDS molecules without their Na+ ions.
Then I filled the simulation box with water molecules. After that, I want
to replace some water molecules with Na+ ions. I ran the
Hi all
Would you please let m eknow f we use 'genconf' after that we must use
'genbox' before applying 'grompp'?
Thanks
Regards
Saly
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Hi all
Would you please let me know how can I remove the following error when I
want to run 'mdrun -v -deffnm H'?
Back Off! I just backed up H.log to ./#H.log.1#
Getting Loaded...
Reading file H.tpr, VERSION 4.5.4 (single precision)
Starting 24 threads
Segmentation fault
Thanks
Regards
Saly
Hi all
In the following you can see the format of H-largebox.gro including my
desired number of atoms, but when I apply the following grompp command with
and with out maxwarn
I see the following error:
---
Program grompp, VERSION 4.5.4
Source
Hi all
When we want to fill a box containing for example 6 molecules we can
not use genbox. We have to use genconf to build it.
genconf -f H.gro -nbox 10 100 100 -o H-largebox.gro
When I use this command as I want a box including 6 molecules are
filled When I open .gro file of the
Hi all
When we want to fill a box containing for example 6 molecules we can
not use genbox. We have to use genconf to build it.
genconf -f H.gro -nbox 10 100 100 -o H-largebox.gro
When I use this command as I want a box including 6 molecules are
filled When I open .gro file of the
Hi Justin
According to the following you said that I should use genconf. Would you
please help me to use it?
Would you please tell me instead of the following command:
genbox -ci H.gro -nmol 8 -box 300 300 300 -p topol.top -o H-box.gro
Which command I should use including genconf and
Hi all
As Justin said to fill a box with 8 molecules I should construct small
boxes containing for example some hundred molecules with 'genconf' and then
build a big box including 8 molecules. Now I want to know how can I use
'genconf' and then genbox, instead of the following command
Hi all
I used genconf and genbox command as the following:
genconf -nbox 50 50 40 -f H.gro -nmolat 100 -o H-box.gro
genbox -cs H-box.gro -nmol 10 -box 100 100 100 -p topol.top -o
H-box_new.gro
But I received:
Reading solvent configuration
Great Red Owns Many ACres of Sand
solvent
Hi
Thanks alot.
With your suggestions my problem was solved.
Saly
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Hi everybody
After using genconf to build a .gro file for example containing 10
molecules, I want to use grompp to minimize the system as the following:
genconf -f H.gro -nbox 10 100 100 -o H-largebox.gro
grompp -f minim.mdp -c H-largebox.gro -p topol.top -o HMin.tpr -maxwarn 1
Although I
Hi,
I want to add 8 of a molecule including 6 atoms. But when I run each of
the following commands I
System total charge: 0.000
Grid: 5 x 5 x 5 cells
nri = 1948, nrj = 22927
Try 63309box_margin = 3t overlap:
Neighborsearching with a cut-off of 3
Table routines are used for coulomb: FALSE
Hi,
I want to add 8 of a molecule including 6 atoms. But when I run each of
the following commands:
genbox -ci H.gro -nmol 8 -box 15 15 15 -p topol.top -o H-box.gro
genbox -ci H.gro -nmol 8 -box 100 100 100 -p topol.top -o H-box.gro
genbox -ci H.gro -nmol 8 -box 150 150 150 -p
Hi
I think the error is not a reason of less memory of my computer. Because in
a supercomputer I see the hollowing error too.
Genbox could be run if I choose the number of atoms less than 5000.
Thanks
Saly
Try 824box_margin = 0.45 overlap:
Neighborsearching with a cut-off of 0.45
Table
Hi all
I want to know about the ability of GROMACS to simulate sulfate in(SO4
(2-)),
Do we can have the ion in our simulation using GROMACS?
Thanks alot
Saly
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Subject: Re: [gmx-users] polarizable water models
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID: 4db80e9c.7010...@anu.edu.au
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 4/27/2011 10:08 PM, saly jackson wrote:
Hi Ivan
Please do not reply
Hi all
I want to simulate using GROMACS.Before I used LAMMPS but it has not
polarizable water models. Therefore I want to use GROMACS.
I need .itp and .mdp files of POL3 water model.
Do you have the files.
Would you please help me.
Thanks alot for your time and attention
Regards
Saly
--
POL3 model, try with other molecular package that
have point polarizable POL3 water (e.g. AMBER)
I hope this help
Ivan
On 04/27/2011 11:04 AM, saly jackson wrote:
Hi all
I want to simulate using GROMACS.Before I used LAMMPS but it has not
polarizable water models. Therefore I want
Hi all
I want to know about the ability of GROMACS to simulate sulfate in(SO4
(2-)),
Do we can have the ion in our simulation using GROMACS?
Thanks alot
Saly
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