Dear users
I tried energy minimization of POPE/POPG bilayer from
http://www.softsimu.net/downloads/pepg-mix.pdb . Process stopped and forces
have not converged to requested precision (output shown below). I used
Gromacs version 2019.2 .
My colleague also used this bilayer before with earlier
Hi,
I am simulating a 5X5 carbon nanotube in the presence of nucleic acids
in Tip3P water. I have made this nanotube using VMD nanotube builder and
made the topology using pdb2gmx. Upto the energy minimization step every
thing was fine but when I proceed for energy minimization I get the carbon
Hi,
The mdp file has pbc= xyz in the last line. In the previous mail it was
written that pbc=full. Plaese ignore it.
Thanks and regards
Soumadwip
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On 6/1/15 8:06 AM, soumadwip ghosh wrote:
Thanks Justin for your quick reply. What are the correct non-bonding
settings for CHARMM to be used in the .mdp file?
http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM
I seem to have to post this information weekly...
Here is
On 6/1/15 9:07 AM, soumadwip ghosh wrote:
Hi Justin,
the snapshot I uploaded in the URL is of the SSDNA-CNT
system after energy minimization step not before it. I stripped off
water and ions from the system for the ease of visualization. I would
be grateful if you suggest me a
On 6/1/15 2:28 AM, soumadwip ghosh wrote:
Hi,
I am simulating a 5X5 carbon nanotube in the presence of nucleic acids
in Tip3P water. I have made this nanotube using VMD nanotube builder and
made the topology using pdb2gmx. Upto the energy minimization step every
thing was fine but when I
Hi Justin,
the snapshot I uploaded in the URL is of the SSDNA-CNT
system after energy minimization step not before it. I stripped off
water and ions from the system for the ease of visualization. I would
be grateful if you suggest me a possible way out.
Regards,
Soumadwip
Research
Thanks Justin for your quick reply. What are the correct non-bonding
settings for CHARMM to be used in the .mdp file?
Here is how the CNT molecule looks like prior to energy minimization.
pre energy min CNT
https://drive.google.com/file/d/0B7SBnQ5YXQSLX0dIOHZjT3p1Y2s/view?usp=sharing
I am not
Of Tsjerk
Wassenaar
Sent: Monday, 18 May 2015 6:21 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] energy minimization problem
Hi Ming Tang,
Can you run in NVT? Then afterwards you can try NPT without position restraints.
Cheers,
Tsjerk
On May 18, 2015 10:14, Ming Tang m21.t
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin
Lemkul
Sent: Sunday, 17 May 2015 7:07 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] energy minimization problem
On 5/16/15 8:30 AM, Ming Tang wrote:
Dear Justin,
I tried to use small time step. First, set dt=0.005ps
...@gromacs.org
Subject: Re: [gmx-users] energy minimization problem
On 5/16/15 8:30 AM, Ming Tang wrote:
Dear Justin,
I tried to use small time step. First, set dt=0.005ps, after running
20ps, I found one chain of the triple helix just went to another water box
totally. I guess
.
-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Tsjerk
Wassenaar
Sent: Monday, 18 May 2015 6:21 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] energy minimization problem
Hi
Subject: Re: [gmx-users] energy minimization problem
Hi Ming Tang,
That's pretty quick. I guess that this is on multiple cores, given the size of
the system. It often helps to equilibrate on a limited number of cores, but I'm
not sure that's feasible.
Did you obtain the model by martinizing
May 2015 6:47 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] energy minimization problem
Hi Ming Tang,
That's pretty quick. I guess that this is on multiple cores, given the size of
the system. It often helps to equilibrate on a limited number of cores, but I'm
not sure that's
Sent: Monday, 18 May 2015 7:04 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] energy minimization problem
Hi Tsjerk,
I used the original structure generated by sabbac.
My computer has 8 cores only, martini simulation looks much faster than full
atomic simulation.
The command I used
...@maillist.sys.kth.se] On Behalf Of Tsjerk
Wassenaar
Sent: Monday, 18 May 2015 6:21 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] energy minimization problem
Hi Ming Tang,
Can you run in NVT? Then afterwards you can try NPT without position restraints.
Cheers,
Tsjerk
On May 18, 2015 10
= xyz
-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin
Lemkul
Sent: Friday, 15 May 2015 11:50 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] energy minimization problem
On 5
-users-boun...@maillist.sys.kth.se
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin
Lemkul
Sent: Friday, 15 May 2015 11:50 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] energy minimization problem
On 5/14/15 9:47 PM, Ming Tang wrote:
Dear Justin,
I saw
...@maillist.sys.kth.se
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of
Justin Lemkul
Sent: Friday, 15 May 2015 11:50 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] energy minimization problem
On 5/14/15 9:47 PM, Ming Tang wrote:
Dear Justin,
I saw
] On Behalf Of Justin
Lemkul
Sent: Friday, 15 May 2015 2:40 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] energy minimization problem
On 5/14/15 3:12 AM, Ming Tang wrote:
Dear all,
I am working with a triple helix containing around 1000 amino acids per chain
using martini force field
On 5/14/15 9:47 PM, Ming Tang wrote:
Dear Justin,
I saw it in the terminal.
Potential Energy = -6.3682131e+05
Maximum force = 1.8876091e+02 on atom 1147
Norm of force = 3.1155257e+00
But, how can I further minimize my protein?
Minimization is not your problem. Post a full
On 1/2/15 11:21 AM, Suman Das wrote:
Hi,
I am trying to simulate a mixture of Choline Chloride+Urea mixture with
33:67 ratio at 298 K. I have taken the force field of choline from this
paper :http://pubs.acs.org/doi/full/10.1021/jp404619x
January 2015 11:21
To: gmx-us...@gromacs.org
Subject: [gmx-users] Energy minimization problem in Choline Chloride+Urea
mixture in Gromacs
Hi,
I am trying to simulate a mixture of Choline Chloride+Urea mixture with
33:67 ratio at 298 K. I have taken the force field of choline from
Hi,
I am trying to simulate a mixture of Choline Chloride+Urea mixture with
33:67 ratio at 298 K. I have taken the force field of choline from this
paper :http://pubs.acs.org/doi/full/10.1021/jp404619x
Hello All
I am trying to perform MD for protein ligand complex in popc lipid with
Charmm36 force field. I follow Justin A. Lemkul tutorial of membrane
protein simulation.
I have successfully perform till InflateGRO followed by energy minimization
step.
perl inflategro.pl em.gro 0.95 POPC 0
Thanks for your reply Justin
The error is now solve but I don't know this is a right way or not.
The step which I perform previously in which I am facing error:
Packing :
1) perl inflategro.pl em.gro 0.95 POPC 0 system_shrink1.gro 5
area_shrink1.dat
2) grompp -f em.mdp -c system_shrink1.gro
On 9/2/14, 10:49 AM, neha bharti wrote:
Thanks for your reply Justin
The error is now solve but I don't know this is a right way or not.
The step which I perform previously in which I am facing error:
Packing :
1) perl inflategro.pl em.gro 0.95 POPC 0 system_shrink1.gro 5
area_shrink1.dat
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