I used -fit or boxcenter or trans or .. any other thing which I though to solve
my problem, but did not work. Would you give me a hint pleaaasssee?
Thanks a lot.
Sincerely,
Shima
On Wednesday, October 16, 2013 4:05 PM, Justin Lemkul jalem...@vt.edu wrote:
On 10/16/13 8:29 AM, Shima
Dear gmx users,
I have a system consist of a lipid bilayer and a peptide. As the initial
configuration, the peptide is located in center of the x-y plane above lipid
bilayer. After running MD, the peptide shows interactions with the polar
groups. It's ok, but the peptide is near one edge of
Hi,
I ran US on an ion through a channel inserted in a bilayer.
I used g_wham and got the profile output. In the visualized profile, I see a
region that the plot shows a flat line and it seems the data is missed there.
Would you please let me know what the reason of missing data is?
Thanks
Hi,
As I know, g_spatial gives me the spatial distribution of a specified group. If
there is any tool to give me the planar distribution of group in x-y graph? Or
if there is any command to help me?
Thanks in advance for your help. I appreciate you.
Sincerely,
Shima
--
gmx-users mailing
Hi,
I want to put position restraint on an ion ,
First made an .itp file of the ion: posre_ion.itp
Then added these line to top file:
#include ./charmm36-modified.ff/ions.itp
#ifdef POSRES_ION
#include ion_posre.itp
#endif
And added the line to mdp file
define = -DPOSRES_ION
But the
#endif
And added the line to mdp file
define = -DPOSRES_ION
Sincerely,
Shima
From: Gaurav Goel gauravgoel...@gmail.com
To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS
users gmx-users@gromacs.org
Sent: Thursday, August 22, 2013 3
file generated by pdb2gmx,
for the ions such as chain A and other moleculetypes ?
Would you give me a hint and help me with it please?
Sincerely,
Shima
-- Forwarded message --
From: Shima Arasteh shima_arasteh2...@yahoo.com
Date: Thu, 22 Aug 2013 03:54:07 -0700 (PDT)
Subject
fcz
85563 1 10 10 10
But it doesnt work, would you please let me know if I had a mistake?
Thanks for your suggestions in earlier messages.
Sincerely,
Shima
- Original Message -
From: Mark Abraham mark.j.abra...@gmail.com
To: Shima Arasteh
-
From: Mark Abraham mark.j.abra...@gmail.com
To: Shima Arasteh shima_arasteh2...@yahoo.com
Cc: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Thursday, August 22, 2013 6:37 PM
Subject: Re: [gmx-users] position restraint
Now you have a [moleculetype] with one atom and hopefully
Sent: Thursday, August 8, 2013 11:08 PM
Subject: Re: [gmx-users] g_WHAM
On 8/8/13 2:37 PM, Shima Arasteh wrote:
g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCalvv
It's the error what get;
File input/output error:
tpr-files.dat
Then a file named tpr-files.dat does not exist
=-1.081898
Why does the g_wham tries to still symmetrize the profile around z=0?
Would you please give me any suggestion?
Sincerely,
Shima
- Original Message -
From: Justin Lemkul jalem...@vt.edu
To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS
users gmx-users
Hi,
I use the
g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kca -sym
I' d like to know if it is possible to symmetrize the profile around a non-zero
point? forexample z=60?
Thanks for your suggestions in advance.
Sincerely,
Shima
--
gmx-users mailing list
Hi,
Would you please let me know if it is possible to get just the first 2
histograms of total 24 histograms by running g_WHAM?
I mean the tpr-files.dat contains only 2 .tpr files of umbrella sampling
simulations and not the all.
I ran such dat file, but doesn't work and gives me an error of
suggestions in advance.
Sincerely,
Shima
- Forwarded Message -
From: Justin Lemkul jalem...@vt.edu
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Thursday, July 25, 2013 4:25 PM
Subject: Re: [gmx-users] Umbrella Sampling _ pulled ion
On 7/25/13 7:52 AM, Shima Arasteh
know your suggestions ?
Sincerely,
Shima
- Original Message -
From: Justin Lemkul jalem...@vt.edu
To: Shima Arasteh shima_arasteh2...@yahoo.com
Cc:
Sent: Wednesday, July 24, 2013 9:41 PM
Subject: Re: [gmx-users] Umbrella Sampling _ pulled ion
On 7/24/13 11:53 AM, Shima Arasteh wrote
Hi,
I am trying to run US on a system composed of lipid bilayer/ ion/ water/
peptide. The peptide is inserted through the lipid bilayer and I' d like to
study the ion conduction through the peptide across the membrane.
In order to do so, I tried to set a specific ion ( Ces with the atom number
result for npt_US or md_US?
Many many thanks for your time and suggestions.
Sincerely,
Shima
- Original Message -
From: Justin Lemkul jalem...@vt.edu
To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS
users gmx-users@gromacs.org
Cc:
Sent: Wednesday, July 24, 2013
Hi,
Would you please let me know how can I make an index file of COM of lipid
membrane?
I guess the position of the COM of the bilayer, but how it is possible to make
an index file of this point?
I want to include this index file as the ref_group in Umbrella Sampling.
Sincerely,
Shima
--
Thanks for your reply.
But would you please tell me what is known for the pull_group line? I mean are
the atom names or resid-s or residue names or know for it?
Sincerely,
Shima
- Forwarded Message -
From: Justin Lemkul jalem...@vt.edu
To: Shima Arasteh shima_arasteh2
] Umbrella Sampling settings
On 7/11/13 5:10 PM, Shima Arasteh wrote:
Thanks for your reply.
But when I don't understand why these extra lines are needed to set when are
not advantageous practically! :-(
There's nothing extra. Everything here has a functional purpose.
-Justin
Sincerely
] Umbrella Sampling settings
On 7/11/13 5:10 PM, Shima Arasteh wrote:
Thanks for your reply.
But when I don't understand why these extra lines are needed to set when are
not advantageous practically! :-(
There's nothing extra. Everything here has a functional purpose.
-Justin
Sincerely
or not? And if it recognizes which ion I mean to be pulled
among many ions exist in the whole system? How is it?
Sincerely,
Shima
- Original Message -
From: Justin Lemkul jalem...@vt.edu
To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS
users gmx-users@gromacs.org
Subject: Re: [gmx-users] Umbrella Sampling settings
On 7/11/13 5:10 PM, Shima Arasteh wrote:
Thanks for your reply.
But when I don't understand why these extra lines are needed to set when
are not advantageous practically!:-(
There's nothing extra.? Everything here has a functional
Dear all,
I see cyclohexane parameters in top par CGenFF files. Would it be correct if
I add this molecule to the rtp file in charmm and then use it as a solvent
rather than for example water?
Generally, how is it possible to add a new solvent to the charmm ff simulations?
Thanks in advance,
Hi,
I want to run Umbrella Sampling on my system. In initial configurations, an ion
is located in center of the window.
Some mdp file settings for running US, as I found in US tutorial are :
; Pull code
pull = umbrella
pull_geometry = distance
pull_dim = N N Y
pull_start
Thanks for your reply.
But when I don't understand why these extra lines are needed to set when are
not advantageous practically! :-(
Sincerely,
Shima
- Original Message -
From: Justin Lemkul jalem...@vt.edu
To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS
/13 7:50 AM, Shima Arasteh wrote:
Thanks for your earlier suggestions.
I used the command
g_select -s npt_6.gro -f md_0_1.trr -select 'resname SOL and within 0.1 of
(36.0, 36.0, 63.0)' -seltype res_com -selrpos res_com -os
to find water molecule around a specified coordinate. But I get
Dear gmx users,
I' d like to get pdb files from trajectory, then used the trjconv,
# trjconv -f trajout.xtc -o out.pdb -sep
It gives fatal error as this:
Can not open file:
topol.tpr
Sincerely,
Shima
--
gmx-users mailing listgmx-users@gromacs.org
Dear gmx users,
I have a 10 ns simulation trajectory, and like to get some particular frames of
it. In fact I want to find the frames in which a specified coordinate is filled
with a water molecule, and then pick that frame as an initial structure for the
next steps.
Is there any script
Dear gmx users,
I have D amino acids in my input .pdb file. The force field which I aim to use,
is CHARMM. I am wondering if I need to modify aminoacids.rtp file? Or it would
be OK if I use the same parameters as L aminoacids for D aminoacids?
Thanks for your suggestions. They would be
, June 19, 2013 3:45 PM
Subject: Re: [gmx-users] InflateGRO methodology deletion radius
On 6/19/13 12:39 AM, Shima Arasteh wrote:
Do you mean the commands of inflateGRO controls the deletion radius?
Yes, that's its purpose. There is a published paper about its algorithm; I
would suggest you read
for your suggestions in advance. Those are really kind of you.
Sincerely,
Shima
- Original Message -
From: Justin Lemkul jalem...@vt.edu
To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS
users gmx-users@gromacs.org
Cc:
Sent: Saturday, June 15, 2013 4:18 PM
Hi,
In Kalp15_DPPC tutorial, when the InflateGRO methodology is applied to pack the
lipids, I need to follow the iteration while the cutoff value changed to 0.
I' d like to know what settings of EM.mdp file are suggested to get the best
results of doing shrinking steps?
When I set the settings
PM, Shima Arasteh wrote:
Would you please tell me which initial deletion radius?
It would be easier for you to provide the exact command(s) you're using. Maybe
you've posted this information before, but this thread (or at least, related
topics) has gone on for a very long time and maybe I'm
I put the output file of shrinking steps after 32 iterations:
https://jumpshare.com/b/5Y6WUGv7OT1sOFzsrWgN
Sincerely,
Shima
- Original Message -
From: Justin Lemkul jalem...@vt.edu
To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS
users gmx-users
suggestions? How would I make a better packed
system without disturbing overlaps or crashes?
Would you please help me?
Thanks for your suggestions and help.
Sincerely,
Shima
- Original Message -
From: Justin Lemkul jalem...@vt.edu
To: Shima Arasteh shima_arasteh2...@yahoo.com
on water oxygen atoms
On 6/10/13 3:37 AM, Shima Arasteh wrote:
Thanks for your reply.
The system I am trying to equilibrate is composed of popc/
peptide/ions/water. I built the system by InflateGRO methodology as you wrote
in kalp-dppc tutorial. The last gro file which gave me
Would you please tell me which initial deletion radius?
And do you mean a smaller scale up factor ( for example 0.90 ) by saying shrink
more slowly?
Sincerely,
Shima
- Original Message -
From: Justin Lemkul jalem...@vt.edu
To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion
Dear gmx users,
I have a POPC/peptide/water/ions system. I ran NVT and then NPT on my system.
I'd prefer to run the equilibrium steps with position restraints on water
oxygen atoms, because the water molecules penetrate the lipid bilayer when
running the equilibrium and I don't want it to
Dear GMX users,
I' d like to put the position restraints on water oxygen atoms.
To do so, I made a water_posre.itp file. Then I modified the top file, as this,
but didn't work:
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx
/Documentation/How-tos/Position_Restraints
On Sun, Jun 2, 2013 at 9:52 AM, Shima Arasteh shima_arasteh2...@yahoo.com
wrote:
Dear GMX users,
I' d like to put the position restraints on water oxygen atoms.
To do so, I made a water_posre.itp file. Then I modified the top file, as
this, but didn't
Hi all,
I want to add CS ions to my system by genion but it seems impossible when go
through the EM.
The molecule section in my top file is:
Protein_chain_A 1
Protein_chain_B 1
POPC 238
SOL 20406
NA 681
CL 702
CS 19
The commands
http://www.gromacs.org/Documentation/Tutorials
Sincerely,
Shima
- Original Message -
From: Sathish Kumar sathishk...@gmail.com
To: Discussion list for GROMACS users gmx-users@gromacs.org
Cc:
Sent: Friday, May 17, 2013 2:08 PM
Subject: [gmx-users] puuling simulations
Sir,
I
Thanks for your reply.
It' s around 5 nano seconds that I ran equilibration time on the system, and
the average pressure I see as a result, seems sensible. However I am not sure
if this criteria is sufficient? Others suggest to evaluate the box-dimension
changes using g_energy code to judge of
the protofibril structures for 100 ns, in another article 25 ns.
Ok, if there is not any universal recipe for it, what do you suggest me? Try
and error?
Sincerely,
Shima
- Original Message -
From: Justin Lemkul jalem...@vt.edu
To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list
the protofibril structures for 100 ns, in another article 25 ns.
Ok, if there is not any universal recipe for it, what do you suggest me? Try
and error?
Sincerely,
Shima
- Original Message -
From: Justin Lemkul jalem...@vt.edu
To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list
Hi,
I am simulating a system composed if POPC , peptide, waters and ions.
I used the InflateGRO methodology to construct the system.
There are 2 phenylalanine residues in my peptide. Each phenyl has 2rings
connected from one side. After inflategro one of the phenyl rings is normal,
but the
Hi,
I am simulating a system composed if POPC , peptide, waters and ions.
I used the InflateGRO methodology to construct the system.
There
are 2 Tryptophan residues in my peptide. Each Tryptophan has 2rings
connected from one side. After inflategro one of the Tryptophan rings is
normal, but
If I skip the pulling code step, how could I generate configurations while
there are one ion in each window? Am I supposed to save my favorite snapshots
during MD simulation trajectory?
Sincerely,
Shima
- Original Message -
From: Justin Lemkul jalem...@vt.edu
To: Shima Arasteh
Hi,
I have a system composed of POPC/peptide/water/ions. I aim to study ion
conduction through the peptide using umbrella sampling.
I built the system and ran EM, NVT, NPT successfully, but have not run md yet.
I' d like to know if the system is required of passing a few nanoseconds md? Or
I
.
This usually means that your system is not well equilibrated.
Would you please give me your suggestions?
Sincerely,
Shima
- Original Message -
From: Shima Arasteh shima_arasteh2...@yahoo.com
To: Justin Lemkul jalem...@vt.edu; gmx-users@gromacs.org
gmx-users@gromacs.org
Cc:
Sent
Hi,
In Umbrella Sampling method, among mdp settings, there is a section where the
pull code settings are defined in:
pull = umbrella: using a harmonic potential to pull
As it is said that with US the path of the permeating ion along thereaction
coordinate is sampled using many discrete
...@vt.edu
To: Discussion list for GROMACS users gmx-users@gromacs.org
Cc:
Sent: Wednesday, May 8, 2013 2:16 AM
Subject: Re: [gmx-users] unstable system
On 5/7/13 2:42 PM, Shima Arasteh wrote:
Hi,
I have run a new npt after energy minimization on my system composed of
water/protein/lipid/ions
...@vt.edu
To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS
users gmx-users@gromacs.org
Cc:
Sent: Wednesday, May 8, 2013 5:07 PM
Subject: Re: [gmx-users] unstable system
On 5/8/13 2:35 AM, Shima Arasteh wrote:
OK.
1. Exact commands given in the preparation protocol
- Original Message -
From: Justin Lemkul jalem...@vt.edu
To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS
users gmx-users@gromacs.org
Cc:
Sent: Friday, April 19, 2013 11:29 PM
Subject: Re: [gmx-users] unstable system
On 4/19/13 2:57 PM, Shima Arasteh wrote:
Thanks so
Hi,
I' like to know if it is possible to get the average RMSD through g_rms
command? Or I need to get it manually?
Thanks for your suggestions.
Sincerely,
Shima
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive
Dear Justin,
About Umbrella sampling tutorial, would you please let me know why you created
an index file contains of chain A and chain B?
Also, what's the meaning of 19 and 20 created by a text editoras groups.txt
file? I can not understand this.
Thanks in advance.
Sincerely,
Shima
--
Hi all,
I aimed to use renumtop script, downloaded from other softwares in GROMACS.org
website.
Does anybody know which language this script is written in? Because I want to
execute this program and write a command as follow, but it doesn't work:
# renumtop topol.top
The error what I get
Hi all,
I aimed to use renumtop script, downloaded from other softwares in GROMACS.org
website.
Does anybody know which language this script is written in? Because I want to
execute this program and write a command as follow, but it doesn't work:
# renumtop topol.top
The error what I
: Justin Lemkul jalem...@vt.edu
To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS
users gmx-users@gromacs.org
Sent: Sunday, April 7, 2013 4:46 PM
Subject: Re: [gmx-users] unstable system
On Sun, Apr 7, 2013 at 1:41 AM, Shima Arasteh shima_arasteh2...@yahoo.com
wrote
users gmx-users@gromacs.org
Cc:
Sent: Friday, April 19, 2013 7:58 PM
Subject: Re: [gmx-users] unstable system
On 4/19/13 11:26 AM, Shima Arasteh wrote:
Hi,
I tried to equilibrate my system by setting timestep=1 fts and decreasing the
position restraints step by step.
But when I go to MDRUN
All right.
And if minimization doesnt fix such a problem, what would be the solution?
However I have not tried it on my own system yet.
Sincerely,
Shima
- Original Message -
From: Justin Lemkul jalem...@vt.edu
To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS
:-)
OK, thanks.
Sincerely,
Shima
- Original Message -
From: Justin Lemkul jalem...@vt.edu
To: Discussion list for GROMACS users gmx-users@gromacs.org
Cc:
Sent: Friday, April 19, 2013 8:42 PM
Subject: Re: [gmx-users] unstable system
On 4/19/13 11:55 AM, Shima Arasteh wrote:
All
list for GROMACS users gmx-users@gromacs.org
Cc:
Sent: Friday, April 19, 2013 8:42 PM
Subject: Re: [gmx-users] unstable system
On 4/19/13 11:55 AM, Shima Arasteh wrote:
All right.
And if minimization doesnt fix such a problem, what would be the solution?
However I have not tried it on my own
Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS
users gmx-users@gromacs.org
Cc:
Sent: Friday, April 19, 2013 10:02 PM
Subject: Re: [gmx-users] unstable system
On 4/19/13 1:18 PM, Shima Arasteh wrote:
Lets check the minim.mdp settings:
( ff applied is charmm36)
define
, April 19, 2013 11:23 PM
Subject: Re: [gmx-users] unstable system
On 4/19/13 2:49 PM, Shima Arasteh wrote:
The energy minimization has been done and the result is as follow:
Steepest Descents converged to Fmax 100 in 8971 steps
Potential Energy = -1.5253394e+06
Maximum force
thanks for your replies.
Sincerely,
Shima
From: Justin Lemkul jalem...@vt.edu
To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS
users gmx-users@gromacs.org
Sent: Sunday, April 7, 2013 4:46 PM
Subject: Re: [gmx-users] unstable system
Hi all,
I have a system of peptide/POPC/water/ions. The energy minimization and NVT
steps has passed successfully. I ran NPT step for around 10 ns with restraints
of protein and P atoms at first nano seconds and then removing them gradually.
I tried to go on MDRUN. I did not remove restraint
Hi all,
I am trying to simulate a system of protein and lipid bilayer ( in this case
POPC). The ff I am using is CHARMM36 and I used related settings from
literature.
I used InflateGRO to pack the lipids around my protein. Then put a position
restraint on my protein and P atoms of POPC.
. I really appreciate
your help.
Sincerely,
Shima
- Forwarded Message -
From: Shima Arasteh shima_arasteh2...@yahoo.com
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Friday, April 5, 2013 6:25 PM
Subject: [gmx-users] water molecule can not be settled
Hi all,
I
coordinate of molecule?
but I seems also impossible becasue PME problem!
So whats the solution?
Sincerely,
Shima
From: Justin Lemkul jalem...@vt.edu
To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS
users gmx-users@gromacs.org
Sent
5, 2013 at 11:19 AM, Shima Arasteh
shima_arasteh2...@yahoo.comwrote:
As I visualized the system, I see a water molecule somewhere between lipid
chains near the protein entrance. This has been happen during NPT. I' d
like to delete this molecule but with such a kind of fatal error this would
Hi,
To inactivate a position restraint, is it enough to make the define command in
mdp file to a comment?
;define= DPOSRES
Sincerely,
Shima
--
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* Please search the archive at
- Original Message -
From: Justin Lemkul jalem...@vt.edu
To: Discussion list for GROMACS users gmx-users@gromacs.org
Cc:
Sent: Tuesday, March 26, 2013 12:02 AM
Subject: Re: [gmx-users] position restraints
On 3/25/13 3:25 PM, Shima Arasteh wrote:
Dear Justin,
As I got, I need to edit
Lemkul jalem...@vt.edu
To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS
users gmx-users@gromacs.org
Cc:
Sent: Tuesday, March 26, 2013 4:16 PM
Subject: Re: [gmx-users] position restraints
On 3/26/13 7:01 AM, Shima Arasteh wrote:
Hi Dear Justin
First of all, I
] position restraints
On Tue, Mar 26, 2013 at 1:01 PM, Shima Arasteh
shima_arasteh2...@yahoo.comwrote:
Have a look at processed topology file here please; I see that position
restraints are brought after chain_A but not brought after chain_B.
With these settings:
; Include chain topologies
From: Justin Lemkul jalem...@vt.edu
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Tuesday, March 26, 2013 10:54 PM
Subject: Re: Fw: [gmx-users] position restraints
On Tue, Mar 26, 2013 at 2:20 PM, Shima Arasteh
shima_arasteh2...@yahoo.comwrote
Hi,
I want to use position restraints on P atom types of POPC, and on my protein
inserted in POPC.
The inserted protein has 2 chains.
1.
I made index files for each chain and then restrained them by these commands:
#make_ndx -f minim.gro -o protein_chain_A.ndx
#genrestr -f minim.gro -o
position_restraints
in a part belonging to a different molecule than you intended to.
Why this doesn't match?? I think POSITION RESTRAINING is making me crazy! :((
Would you please help me?
Thanks for help.
Sincerely,
Shima
- Original Message -
From: Justin Lemkul jalem...@vt.edu
To: Shima Arasteh
To: Discussion list for GROMACS users gmx-users@gromacs.org
Cc:
Sent: Monday, March 25, 2013 10:13 PM
Subject: Re: [gmx-users] position restraints
On 3/25/13 1:40 PM, Shima Arasteh wrote:
Believe me I add this line to mdp file as you wrote in KALP-15-DPPC.
I believe what I see. If you're trying to re
Would you please let me know that what subject I need to look for through
manual or threads? Making index groups of multiple atoms?
Thanks for your suggestions.
Sincerely,
Shima
- Original Message -
From: Justin Lemkul jalem...@vt.edu
To: Shima Arasteh shima_arasteh2...@yahoo.com
@gromacs.org
Cc:
Sent: Monday, March 25, 2013 11:20 PM
Subject: Re: [gmx-users] position restraints
On 3/25/13 2:47 PM, Shima Arasteh wrote:
Would you please let me know that what subject I need to look for through
manual or threads? Making index groups of multiple atoms?
What you need
: Justin Lemkul jalem...@vt.edu
To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS
users gmx-users@gromacs.org
Cc:
Sent: Monday, March 25, 2013 11:34 PM
Subject: Re: [gmx-users] position restraints
On 3/25/13 3:00 PM, Shima Arasteh wrote:
Yes, you are right. Because I have
AM
Subject: Re: [gmx-users] position restraints
On 3/25/13 3:25 PM, Shima Arasteh wrote:
Dear Justin,
As I got, I need to edit the lipid_posre.itp file. To do so, I need to change
numbering of position restraining in lipid_posre.itp file to what they are in
their original itp file: In my
Hi,
I am solving a protein in water. This protein has a charge of +3.
After solvation there is 3272 water molecules.
Next, I use genion command to add NACL 1M and 3 extra CL ions to neutralize the
system.
#genion -s ions.tpr -o cyclic_solv_ions.gro -p topol.top -nname CL -nn 3 -conc 1
After
In fact the genion does not add the neutralizing CL ions to gro file! Why?
How can I solve this problem?
Would you please help me?
Sincerely,
Shima
- Original Message -
From: Shima Arasteh shima_arasteh2...@yahoo.com
To: Discussion list for GROMACS users gmx-users@gromacs.org
Cc
Thanks!
I did! :-)
Sincerely,
Shima
From: Mark Abraham mark.j.abra...@gmail.com
To: Discussion list for GROMACS users gmx-users@gromacs.org
Cc: Shima Arasteh shima_arasteh2...@yahoo.com
Sent: Sunday, March 24, 2013 9:50 PM
Subject: Re: [gmx-users] Re: gro
Hi,
I need to set position restraints on phosphorus head groups of lipids in
addition of protein.
In mdp file I added two lines:
define = -DPOSRES
define= -DPOSRES_LIPID
But I get the error that multiple define assignments are not allowed. Is the
define= -DPOSRES_LIPID is enough for both
is that, to eliminating the position restraints in MDRUN,
is it supposed to reduce the force on atoms before mdrun gradually? Or it is ok
to reduce it in MD step?
Thanks for your suggestions.
Sincerely,
Shima
- Original Message -
From: Justin Lemkul jalem...@vt.edu
To: Shima Arasteh
.
Sincerely,
Shima
From: Justin Lemkul jalem...@vt.edu
To: Shima Arasteh shima_arasteh2...@yahoo.com
Cc: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Tuesday, March 19, 2013 9:11 PM
Subject: Re: [gmx-users] Top file modification
On Tue, Mar 19
Hi,
I am simulating a system of POPC/Water/Ions/protein.
Ions are 1 M NaCL and 3 CL atoms to neutralize the system.
In NVT step, I have coupling groups as :
tc-grps = Protein POPC SOL_CL
comm_grps = Protein_POPC SOL_CL
when I run the grompp for NVT, I get the error that the
So accordance with Justin's and your statement, SOL_CL_NA coupling would be a
proper option. right?
Thanks for your suggestions
Sincerely,
Shima
From: Gunther Lukat g.lu...@gmx.net
To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS
Dear gmx users,
I have modified the top file of my input.pdb. In this modification I have
deleted 2 atoms, bonds, and diedrals which these deldeted atoms are involved.
The atom numbers of deleted atoms are 2 and 3.
IN grompp I get a fatal error that the top file has not a consecutive numbers
Dear users,
I modified my top file, because I didn't want some bonds. So I deleted them and
changed charges on some atoms.
I want to go on with such a top file, however I am not sure that these changes
are implemented properly or not. Would you please let me know if what I did is
right or
...@vt.edu
To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS
users gmx-users@gromacs.org
Sent: Tuesday, March 19, 2013 8:51 PM
Subject: Re: [gmx-users] Top file modification
On Tue, Mar 19, 2013 at 1:07 PM, Shima Arasteh shima_arasteh2...@yahoo.com
wrote:
Dear
I be sure that I have added all modifications completely?
Sincerely,
Shima
From: Justin Lemkul jalem...@vt.edu
To: Shima Arasteh shima_arasteh2...@yahoo.com
Sent: Tuesday, March 19, 2013 9:00 PM
Subject: Re: [gmx-users] Top file modification
On Tue, Mar 19
Dears,
There is term of function for each 4 atoms in dihedral section in top file. How
this function is defined? To add extra dihedrals manually, I need to add
function too.
Thanks.
Sincerely,
Shima
--
gmx-users mailing listgmx-users@gromacs.org
As I found up to now, func 2 is related to improper dihedrals. How can I find
improper dihedrals? Can I not add them?
Sincerely,
Shima
- Original Message -
From: Shima Arasteh shima_arasteh2...@yahoo.com
To: Discussion list for GROMACS users gmx-users@gromacs.org
Cc:
Sent: Tuesday
the settings
incorrectly?
What would be other potent problems?
Please help me.
Thanks for your help.
Sincerely,
Shima
- Original Message -
From: Justin Lemkul jalem...@vt.edu
To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS
users gmx-users@gromacs.org
Cc
Thanks for all your replies.
But I' d like to know what the meanings of S and D are? Why sometimes we should
write DPOSRE, sometimes POSRE, and sometimes DPOSRES?
Sincerely,
Shima
From: Shima Arasteh shima_arasteh2...@yahoo.com
To: Justin Lemkul jalem
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