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 wrote:
On 10/16/13 8:29 AM, Shima Arasteh wrote
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 t
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 li
-
From: Mark Abraham
To: Shima Arasteh
Cc: Discussion list for GROMACS users
Sent: Thursday, August 22, 2013 6:37 PM
Subject: Re: [gmx-users] position restraint
Now you have a [moleculetype] with one atom and hopefully a position
restraint. But its [position_restraints] wants to act on atom 85563
traints ]
; i funct fcx fcy 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
To: Shima Arasteh
ion? I don't see any itp 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
Date: Thu, 22 Aug 2013 03:54:07 -0700 (PDT)
Subj
t;ion_posre.itp"
#endif
And added the line to mdp file
define = -DPOSRES_ION
Sincerely,
Shima
From: Gaurav Goel
To: Shima Arasteh ; Discussion list for GROMACS
users
Sent: Thursday, August 22, 2013 3:39 PM
Subject: Re: [gmx-users] position re
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
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 n
=-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
To: Shima Arasteh ; Discussion list for GROMACS
users
Cc:
Sent: Friday, August 9, 2013 2:40 PM
Subject: Re
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 listgmx-users@gromacs
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
Sincerely,
Shima
- Original Message -
From: Justin Lemkul
To: Shima Arasteh ; Discussion list for GROMACS
users
Cc:
Sent: Thursday, August 8, 20
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 n
suggestions in advance.
Sincerely,
Shima
- Forwarded Message -
From: Justin Lemkul
To: Discussion list for GROMACS users
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 wrote:
> After running for 100 ps
know your suggestions ?
Sincerely,
Shima
- Original Message -
From: Justin Lemkul
To: Shima Arasteh
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:
> Yes, Thanks.
>
> Would you
odd result for npt_US or md_US?
Many many thanks for your time and suggestions.
Sincerely,
Shima
- Original Message -
From: Justin Lemkul
To: Shima Arasteh ; Discussion list for GROMACS
users
Cc:
Sent: Wednesday, July 24, 2013 8:05 PM
Subject: Re: [gmx-users] Umbrella Sampling _ pulle
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
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
To: Shima Arasteh ; Discussion list for GROMACS
users
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
--
Original Message -
> From: Justin Lemkul
> To: Discussion list for GROMACS users
> Cc:
> Sent: Friday, July 12, 2013 1:41 AM
> Subject: Re: [gmx-users] Umbrella Sampling settings
>
>
>
> On 7/11/13 5:10 PM, Shima Arasteh wrote:
>> >Thanks for your re
r 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
To: Shima Arasteh ; Discussion list for GROMACS
users
Cc:
Sent: Friday, July 12, 2013 8:16 PM
Subject: Re:
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
>
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
>
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
To: Shima Arasteh ; Discussion list for GROMACS
users
Cc:
Sent: Friday, July 12, 2
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
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,
but didn't find the problem with my command.
Thanks in advance.
Sincerely,
Shima
- Original Message -
From: Justin Lemkul
To: Discussion list for GROMACS users
Cc:
Sent: Monday, July 8, 2013 9:14 PM
Subject: Re: [gmx-users] Get some specific frames of traj
On 7/8/13 7:50 AM,
r or input inconsistency:
selection(s) could not be parsed
Would you please help me with this command? I have not yet tried g_select
command.
Thanks in advance.
Sincerely,
Shima
From: Justin Lemkul
To: Shima Arasteh ; Discussion list for GROMACS
users
Sent: Sund
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 implem
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
http://lists.gromacs.org/mailman/lis
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 apprec
-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 and understand i
for your suggestions in advance. Those are really kind of you.
Sincerely,
Shima
- Original Message -
From: Justin Lemkul
To: Shima Arasteh ; Discussion list for GROMACS
users
Cc:
Sent: Saturday, June 15, 2013 4:18 PM
Subject: Re: [gmx-users] InflateGRO methodology deletion radius
On
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 a
I put the output file of shrinking steps after 32 iterations:
https://jumpshare.com/b/5Y6WUGv7OT1sOFzsrWgN
Sincerely,
Shima
- Original Message -
From: Justin Lemkul
To: Shima Arasteh ; Discussion list for GROMACS
users
Cc:
Sent: Tuesday, June 11, 2013 3:25 PM
Subject: Re: [gmx
in
em_shrink32.gro, there are many improper overlaps and acyl penetration to the
protein, disgusting!
Sincerely,
Shima
- Original Message -
From: Justin Lemkul
To: Discussion list for GROMACS users
Cc:
Sent: Monday, June 10, 2013 11:12 PM
Subject: Re: [gmx-users] restraints on wat
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
To: Shima Arasteh ; Discussion list for GROMACS
users
Cc:
Sent: Monday
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 the acceptable APL,
&g
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
To: Shima Arasteh ; Discussion list for GROMACS
users
Cc:
Sent
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 happe
I just applied genrestr command:
#genrestr -f minim.gro -o water_posre.itp -fc 10 10 10
And then I just chose the water to create the water_posre.itp.
Would not that work?
Sincerely,
Shima
From: Mark Abraham
To: Shima Arasteh ; Discussion list
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 fcy
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 t
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
To: Shima Arasteh ; 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 Tryptophan residues in my peptide. Each Tryptophan has 2rings
connected from one side. After inflategro one of the Tryptophan 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 phenylalanine residues in my peptide. Each phenyl has 2rings
connected from one side. After inflategro one of the phenyl rings is normal,
but the other
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
To: Shima Arasteh ; Discussion list for GROMACS
users
Cc:
Sent: Friday, May
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
To: Shima Arasteh ; Discussion list for GROMACS
users
Cc:
Sent: Friday, May 17
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 s
http://www.gromacs.org/Documentation/Tutorials
Sincerely,
Shima
- Original Message -
From: Sathish Kumar
To: Discussion list for GROMACS users
Cc:
Sent: Friday, May 17, 2013 2:08 PM
Subject: [gmx-users] puuling simulations
Sir,
I want to do pulling simulations for membrane p
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 mi
f the domain decomposition cell of their charge group in
dimension x.
This usually means that your system is not well equilibrated.
Would you please give me your suggestions?
Sincerely,
Shima
- Original Message -
From: Shima Arasteh
To: Justin Lemkul ; "gmx-users@gromacs.org"
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 window
l
To: Shima Arasteh ; Discussion list for GROMACS
users
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 (EM and equilibration)
>
> EM:
> #
: Discussion list for GROMACS users
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.
> After a few nanosec
Shima
- Original Message -
From: Justin Lemkul
To: Shima Arasteh ; Discussion list for GROMACS
users
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 much for your replies. I appreciate you.
> Do you
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
--
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* Please search the archive at
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 get
: [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 = 9.2729095e+01 on a
:
1 particles communicated to PME node 4 are more than 2/3 times the cut-off out
of the domain decomposition cell of their charge group in dimension x.
So needs more npt?
Thanks for your suggestions in advance.
Sincerely,
Shima
- Original Message -
From: Justin Lemkul
To: Shima Aras
users
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 system yet.
>
>
:-)
OK, thanks.
Sincerely,
Shima
- Original Message -
From: Justin Lemkul
To: Discussion list for GROMACS users
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
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
To: Shima Arasteh ; Discussion list for GROMACS
users
Cc:
Sent: Friday, April 19, 2013
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 step,
: Justin Lemkul
To: Shima Arasteh ; Discussion list for GROMACS
users
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
wrote:
Hi all,
>
> I have a system of peptide/POPC/water/ions. The energy minimization a
thanks for your replies.
Sincerely,
Shima
From: Justin Lemkul
To: Shima Arasteh ; Discussion list for GROMACS
users
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
wrote
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 o
You mean start over the NPT step?
Sincerely,
Shima
- Original Message -
From: Justin Lemkul
To: Discussion list for GROMACS users
Cc:
Sent: Friday, April 5, 2013 7:50 PM
Subject: Re: Fw: [gmx-users] water molecule can not be settled
On Fri, Apr 5, 2013 at 11:19 AM, Shima Arasteh
to change coordinate of molecule?
but I seems also impossible becasue PME problem!
So whats the solution?
Sincerely,
Shima
From: Justin Lemkul
To: Shima Arasteh ; Discussion list for GROMACS
users
Sent: Friday, April 5, 2013 7:42 PM
Subject: Re: Fw: [gmx-us
ently. I really appreciate
your help.
Sincerely,
Shima
- Forwarded Message -
From: Shima Arasteh
To: Discussion list for GROMACS users
Sent: Friday, April 5, 2013 6:25 PM
Subject: [gmx-users] water molecule can not be settled
Hi all,
I am trying to simulate a system of protei
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. With
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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http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.
From: Justin Lemkul
To: Discussion list for GROMACS users
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
wrote:
> The inclusion part was edited again in original top file. I d
position restraints
On Tue, Mar 26, 2013 at 1:01 PM, Shima Arasteh
wrote:
>
>
>
> 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 topol
Lemkul
To: Shima Arasteh ; Discussion list for GROMACS
users
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 request you that not to shout at me! I am so s
ns with the same
numbering.
Sincerely,
Shima
Sincerely,
Shima
- Original Message -
From: Justin Lemkul
To: Discussion list for GROMACS users
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
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 case popc.itp fil
: Justin Lemkul
To: Shima Arasteh ; Discussion list for GROMACS
users
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 read the include mechanism in website many
> times, but
, 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 to understand is how the
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
To: Shima Arasteh ; Discussion list for GROMACS
users
Cc
se let me know.
Sincerely,
Shima
- Original Message -
From: Justin Lemkul
To: Discussion list for GROMACS users
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
inserted topology section "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
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 protein_
Thanks!
I did! :-)
Sincerely,
Shima
From: Mark Abraham
To: Discussion list for GROMACS users
Cc: Shima Arasteh
Sent: Sunday, March 24, 2013 9:50 PM
Subject: Re: [gmx-users] Re: gro does not match top
On Sun, Mar 24, 2013 at 2:32 PM, Justin Lemkul
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
To: Discussion list for GROMACS users
Cc:
Sent: Sunday, March 24, 2013 5:16 PM
Subject: gro
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 t
s 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
To: Shima Arasteh ; Discussio
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 pr
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
an
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
To: Shima Arasteh ; Discussion list for GROMACS
users
Sent: Thursday, March 21, 2013
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 615
.
Sincerely,
Shima
From: Justin Lemkul
To: Shima Arasteh
Cc: Discussion list for GROMACS users
Sent: Tuesday, March 19, 2013 9:11 PM
Subject: Re: [gmx-users] Top file modification
On Tue, Mar 19, 2013 at 1:36 PM, Shima Arasteh
wrote:
Would you please let me
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
To: Discussion list for GROMACS users
Cc:
Sent: Tuesday, March 19, 2013 9:46 PM
Subject: [gmx-users
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
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How would I be sure that I have added all modifications completely?
Sincerely,
Shima
From: Justin Lemkul
To: Shima Arasteh
Sent: Tuesday, March 19, 2013 9:00 PM
Subject: Re: [gmx-users] Top file modification
On Tue, Mar 19, 2013 at 1:28 PM, Shima Arast
: Shima Arasteh ; Discussion list for GROMACS
users
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
wrote:
>
> Dear users,
>
>I modified my top file, because I didn't want some bonds. So I d
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 n
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