On 4/2/13 6:07 AM, alex rayevsky wrote:
Dear All!
I have a doubt about the rightness of ligand/molecule integration in the
topology file. I'm using an amber (tleap) or swissparam.ch to build a
topology of the residue (modified trna). Is it neccessary to generate a
position restrain file (genres
Dear All!
I have a doubt about the rightness of ligand/molecule integration in the
topology file. I'm using an amber (tleap) or swissparam.ch to build a
topology of the residue (modified trna). Is it neccessary to generate a
position restrain file (genrestr program) for this residue or not? I've
st
On Tue, Mar 26, 2013 at 2:33 PM, Shima Arasteh
wrote:
> Thanks for all your explanations.
> What I get as a conclusion is this:
> itp files are dependent to the numbering of aoms in molecule type
> directive and not any other things! Each posre.itp file created by genrestr
> should be in consisten
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
On Tue, Mar 26, 2013 at 2:20 PM, Shima Arasteh
wrote:
> The inclusion part was edited again in original top file. I dont know why
> I had written that! Sorry.
> But about last itp files, which you mentioned that they are created
> incorrectly, 1) I 'd like to know what itp file should be created?
otein_chain_A 1
Protein_chain_B 1
POPC 238
SOL 18706
NA 615
CL 617
Sincerely,
Shima
- Original Message -
From: Justin Lemkul
To: Discussion list for GROMACS users
Cc:
Sent: Tuesday, March 26, 2013 9:55 PM
Subject: Re: Fw: [gmx-users]
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 topologies
> #ifdef POSRES
> #include "topol_Protei
On 3/26/13 8:39 AM, Shima Arasteh wrote:
No, You have not shouted at me, never! But sometimes I think that I deserve to
be shouted !!
I deeply appreciate your patience and attention. Thanks for your time and your
replies.
In my protein, chains A and B are identical.
If they are identical,
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
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 sorry to ask you
questions about position restraints again!
I haven't done any shouting, but statements like this seem to imply that I have.
The point of this forum is p
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
Ohhh...! :-)
I could not get it on my own independently!
Thanks for all your explanation! Many many thanks.
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
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 file.
Am I right?
More or less, bu
: 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
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 I dont undrestand it in deep! :-(
I may need to study more.
I would again suggest focusing more on the position restraints contents
themselves. Your formulation
, 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
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 position restraint mechanism works. If
you know that, you can make .itp files
:
Sent: Monday, March 25, 2013 10:22 PM
Subject: Re: [gmx-users] position restraints
On 3/25/13 1:50 PM, Shima Arasteh wrote:
> Yes sir!
>
> What I have in my top file is :
> ; Include forcefield parameters
> #include "./charmm36-modified.ff/forcefield.itp"
>
&g
On 3/25/13 1:50 PM, Shima Arasteh wrote:
Yes sir!
What I have in my top file is :
; Include forcefield parameters
#include "./charmm36-modified.ff/forcefield.itp"
; Include chain topologies
#include "topol_Protein_chain_A.itp"
#ifdef POSRES
#include "protein_chain_A_posre.itp"
#endif
#includ
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
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-type from memory what's in your
topology and/or .mdp file, that's not productive. Please copy and paste to make
efficient use of ever
-
From: Justin Lemkul
To: Shima Arasteh ; Discussion list for GROMACS
users
Cc:
Sent: Monday, March 25, 2013 8:52 PM
Subject: Re: [gmx-users] position restraints
On 3/25/13 12:06 PM, Shima Arasteh wrote:
> Hi,
>
> I want to use position restraints on P atom types of POPC, and on my pro
On 3/25/13 12:06 PM, Shima Arasteh wrote:
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_
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_
On Mon, Mar 18, 2013 at 8:24 AM, Shima Arasteh
wrote:
> Yes, I overcome the last problems and I could see the pos.rest energy term
> in my log file.
> In order to create the itp files to include in top file, I opened the gro
> file which I entered as an input in my mdrun command. How might I check
for GROMACS
> users
> Cc:
> Sent: Saturday, March 16, 2013 12:24 AM
> Subject: Re: Fw: Fwd: [gmx-users] position restraints
>
>
>
> On 3/15/13 8:50 AM, Shima Arasteh wrote:
>> Dear users,
>>
>>
>> Although I put the position restraints on backbone, I g
n't matter at all, as long as you
> are consistent in invoking it.
>
> -Justin
>
>
>
>>
>> Sincerely,
>> Shima
>>
>>
>> __**__
>> From: Shima Arasteh
>> To: Justin Lemkul ; Discussion list for GROMACS us
moving normally when you think they
are being restrained.
-Justin
Thanks for your suggestions in advance.
Sincerely,
Shima
- Original Message -
From: Justin Lemkul
To: Shima Arasteh ; Discussion list for GROMACS users
Cc:
Sent: Saturday, March 16, 2013 12:24 AM
Subject: Re: Fw:
nday, March 18, 2013 10:35 AM
Subject: Re: Fwd: Fw: Fwd: [gmx-users] position restraints
To solve the problem, I changed all DPOSREs in if statments to POSRE. Again I get the
fatal error. This error states that I have inserted topology section
"position_restraints" in a wrong place.
een what it is.
-Justin
What would be other potent problems?
Please help me.
Thanks for your help.
Sincerely,
Shima
- Original Message -
From: Justin Lemkul
To: Shima Arasteh ; Discussion list for GROMACS users
Cc:
Sent: Sunday, March 17, 2013 5:19 PM
Subject: Re: Fwd: Fw:
ible by using a greater fc ?
Is it sensible?
Thanks for your suggestions in advance.
Sincerely,
Shima
- Original Message -
From: Justin Lemkul
To: Shima Arasteh ; Discussion list for GROMACS
users
Cc:
Sent: Saturday, March 16, 2013 12:24 AM
Subject: Re: Fw: Fwd: [gmx-users] posi
users
Sent: Monday, March 18, 2013 10:35 AM
Subject: Re: Fwd: Fw: Fwd: [gmx-users] position restraints
To solve the problem, I changed all DPOSREs in if statments to POSRE. Again I
get the fatal error. This error states that I have inserted topology section
"position_restraints" in a
d: Fw: Fwd: [gmx-users] position restraints
On 3/17/13 6:50 AM, Shima Arasteh wrote:
> Thanks for your replies.
> As you suggested, I did as follows:
> 1. made index groups of two chains of my protein
> 2.Then applied genrestr in this command to generate 2 itp files:
On 3/17/13 6:50 AM, Shima Arasteh wrote:
Thanks for your replies.
As you suggested, I did as follows:
1. made index groups of two chains of my protein
2.Then applied genrestr in this command to generate 2 itp files:
chainA_posre.itp and chainB_posre.itp
#genrestr -f system_solv_ions.gro -o cha
by mistake?
Thanks in advance.
Sincerely,
Shima
From: Justin Lemkul
To: Discussion list for GROMACS users
Sent: Saturday, March 16, 2013 4:06 PM
Subject: Re: Fwd: Fw: Fwd: [gmx-users] position restraints
On 3/16/13 8:34 AM, Shima Arasteh wrote:
> Thanks.
> As I
On 3/16/13 8:34 AM, Shima Arasteh wrote:
Thanks.
As I understood from your emails, I need to make index groups of separate
chains of my protein, use the index file in order to use in genrestr command
and then include the specific itp files for each groups in top file?
Do you mean this? Am I r
Subject: Re: Fwd: Fw: Fwd: [gmx-users] position restraints
On 3/16/13 7:09 AM, Shima Arasteh wrote:
> Do you mean that I need to make 2 backbone_posre.itp files for 2 chains?
> It would not be possible because I don't see any option for seperate chains
> when running genrestr c
On 3/16/13 7:09 AM, Shima Arasteh wrote:
Do you mean that I need to make 2 backbone_posre.itp files for 2 chains?
It would not be possible because I don't see any option for seperate chains
when running genrestr command.
You need to provide a sensible index group to genrestr to create such
asteh ; Discussion list for GROMACS
users
Sent: Saturday, March 16, 2013 2:21 PM
Subject: Re: Fwd: Fw: Fwd: [gmx-users] position restraints
On Sat, Mar 16, 2013 at 9:40 AM, Shima Arasteh
wrote:
As you said I changed define in mdp file to define=-DPOSRE .
>
>I also included backbone.itp f
n/Errors
>
> Would you please give me suggestions?
>
The error message already did... Your chains are not identical. You are
applying the same position restraints file to them. GROMACS doesn't know
what you mean.
Mark
>
> Thanks in advance.
>
> Sincerely,
> Shima
>
please give me suggestions?
Thanks in advance.
Sincerely,
Shima
- Original Message -
From: Justin Lemkul
To: Shima Arasteh ; Discussion list for GROMACS
users
Cc:
Sent: Saturday, March 16, 2013 12:25 AM
Subject: Re: Fwd: Fw: Fwd: [gmx-users] position restraints
On 3/15/13 9:43 AM
please give me suggestions?
Thanks in advance.
Sincerely,
Shima
- Original Message -
From: Justin Lemkul
To: Shima Arasteh ; Discussion list for GROMACS
users
Cc:
Sent: Saturday, March 16, 2013 12:25 AM
Subject: Re: Fwd: Fw: Fwd: [gmx-users] position restraints
On 3/15/13 9:43 AM
applied. A position restraint energy term is written to
the .log and .edr files. If it's not there, you're not applying restraints.
-Justin
Thanks in advance.
Your suggestions would be appreciated.
Shima
-- Forwarded message --
From: Shima Arasteh
Date: Fri, 15 Ma
On 3/15/13 8:50 AM, Shima Arasteh wrote:
Dear users,
Although I put the position restraints on backbone, I get RMSD around 0.2 nm.
Is it usual?
No, 0.2 nm is very high. With position restraints, offhand I would think around
0.05 nm or less would be indicative of proper restraints.
Thi
d you please suggest me how I
can apply position restraints effectively?
Thanks in advance.
Your suggestions would be appreciated.
Shima
-- Forwarded message --
From: Shima Arasteh
Date: Fri, 15 Mar 2013 05:50:09 -0700 (PDT)
Subject: Fw: Fwd: [gmx-users] position restraints
To: Discussi
Dear users,
Although I put the position restraints on backbone, I get RMSD around 0.2 nm.
Is it usual?
This deviation is just for a minimization step only. I' m on doubt about
keeping the backbone in a fix secondary structure.
I' d prefer to restraint the backbone completely. Is it possible?
Restraints allow, by definition, for slight deviations.
Erik
On Mar 14, 2013, at 12:51 PM, Shima Arasteh wrote:
Dear gmx users,
I want to use restraints on backbone of my protein to keep its
secondary structure during minimization and equilibration steps. To
do so, I generated backbone-re
Dear gmx users,
I want to use restraints on backbone of my protein to keep its secondary
structure during minimization and equilibration steps. To do so, I generated
backbone-restrain.itp and then included it to top file. Next, added define =
-DPOSRES to minim.mdp file.
After minimization, whe
On 7/16/12 5:36 AM, Raj wrote:
Hi all,
It may be naive but I would like to get some clear explanation in SMD ( COM
pulling) reg. The question is, Before performing the COM-pulling (incase of
protein ligand complex) do we need to position restrain the ligand using
genrestr and then add the to
Hi all,
It may be naive but I would like to get some clear explanation in SMD ( COM
pulling) reg. The question is, Before performing the COM-pulling (incase of
protein ligand complex) do we need to position restrain the ligand using
genrestr and then add the topology to the topol.top file. If not
On Tue, May 29, 2012 at 12:21 PM, Justin A. Lemkul wrote:
>
>
> On 5/29/12 6:52 AM, Steven Neumann wrote:
>
>> Ok. My topology:
>>
>> ; Include forcefield parameters
>> #include "./charmm27.ff/forcefield.itp"
>>
>> ; Include ligand topology
>> #include "ligand1.itp"
>>
>> ; Include Position restr
On 5/29/12 6:52 AM, Steven Neumann wrote:
Ok. My topology:
; Include forcefield parameters
#include "./charmm27.ff/forcefield.itp"
; Include ligand topology
#include "ligand1.itp"
; Include Position restraint file
#ifdef POSRES_1
#include "posre_ligand1.itp"
#endif
; Include ligand topology
Ok. My topology:
; Include forcefield parameters
#include "./charmm27.ff/forcefield.itp"
; Include ligand topology
#include "ligand1.itp"
; Include Position restraint file
#ifdef POSRES_1
#include "posre_ligand1.itp"
#endif
; Include ligand topology
#include "ligand2.itp"
; Include Position re
On 5/28/12 10:48 AM, Steven Neumann wrote:
Dear Gmx Users,
I am fighting with the position restraints. My system cosnsists of 6 ligands -
all of them have the same topology - ligand.itp. I want to:
1. Run NPT restraining all of ligands (easy: -DPOSRES_L, ifdef POSRE_L, posre
ligand1.itp
2. Re
Dear Gmx Users,
I am fighting with the position restraints. My system cosnsists of 6
ligands - all of them have the same topology - ligand.itp. I want to:
1. Run NPT restraining all of ligands (easy: -DPOSRES_L, ifdef POSRE_L,
posre ligand1.itp
2. Restrain 5 of them and pull one of them away.
He
On 4/26/12 1:59 PM, Dariush Mohammadyani wrote:
Thanks dear Justin.
No, the protein is moving in right direction, but I am going to restrain any
changing the position and then monitory these movements during MD run.
I could see the Pos. Res. works in md.log file.
Then I don't understand what
Thanks dear Justin.
No, the protein is moving in right direction, but I am going to restrain
any changing the position and then monitory these movements during MD run.
I could see the Pos. Res. works in md.log file.
Regards,
Dariush
On Thu, Apr 26, 2012 at 1:38 PM, Justin A. Lemkul wrote:
>
>
On 4/26/12 1:35 PM, Dariush Mohammadyani wrote:
Dear All,
I am using CG-MD using MARTINI forcefield. The system contains Protein and lipid
bilayer. Although I used:
define = -DPOSRES
components in system were moving around and interact with each other. Then, I
cannot do NVT or NPT equilibration
Dear All,
I am using CG-MD using MARTINI forcefield. The system contains Protein and
lipid bilayer. Although I used:
define = -DPOSRES
components in system were moving around and interact with each other. Then,
I cannot do NVT or NPT equilibration.
Could you please let me know how can I control thi
Hey :)
A sed oneliner to generate position_restraints for the first
moleculetype in a file, using an fc of 200:
sed -n -e '/\[ *atoms *\]/,/^ *\[/{/^\( *[0-9]\+\) .*/s//\1 1 200 200
200/p}' -e '/\[ *atoms *\]/i[ position_restraints ]' molecule.itp
Cheers,
Tsjerk
On Wed, Mar 28, 2012 at 3:33
True. Even more so if the position restraints file can be generated with basic
Bash commands in under a minute.
Jernej
On 28. mar. 2012, at 20:16, gmx-users-requ...@gromacs.org wrote:
> It's pretty rare to have more than a handful of [moleculetype] sections,
> each of which would want customiz
On 28/03/2012 7:39 PM, Jernej Zidar wrote:
On Wed, Mar 28, 2012 at 16:17, wrote:
See the warning in genrestr -h.
If all you're doing is adding a single atom of position restraint per
moleculetype, you can do that by hand faster than using make_ndx and
genrestr and adding the #include.
Mark
T
On Wed, Mar 28, 2012 at 16:17, wrote:
> See the warning in genrestr -h.
>
> If all you're doing is adding a single atom of position restraint per
> moleculetype, you can do that by hand faster than using make_ndx and
> genrestr and adding the #include.
>
> Mark
This in turn means genrestr is use
On 28/03/2012 6:52 PM, Jernej Zidar wrote:
Hi.
After successfully importing a CHARMM-generated PDB file to GROMACS
I set out to do some short simulations. While all calculations
finished without a problem if everything but the water molecules were
fixed.
Removing the position restraints le
Hi.
After successfully importing a CHARMM-generated PDB file to GROMACS
I set out to do some short simulations. While all calculations
finished without a problem if everything but the water molecules were
fixed.
Removing the position restraints led to the system blowing up. Using
J. Lemkul's t
On 30/10/2011 11:04 AM, Yun Shi wrote:
Hello all,
I am using amber99SB to model an antibody with organic ligands.
I know we could choose to restrain all atoms or only heavy atoms
during the equilibration. But I wonder if this really matters for my
system. As far as I know, equilibration is ai
Hello all,
I am using amber99SB to model an antibody with organic ligands.
I know we could choose to restrain all atoms or only heavy atoms during the
equilibration. But I wonder if this really matters for my system. As far as
I know, equilibration is aimed at getting the temperature and pressure
Hi Justin,
Ok - the .tpr file only lists the atoms from the molecule type. I get it
now. Thanks again!
Craig
On 16 Jun 2011, at 12:58, Justin A. Lemkul wrote:
Craig Kitchen wrote: Dear All, My system consists of 32 identical molecules
(with 91 atoms per molecule). I would like to apply
You already are. The [position_restraints] directive is applied to the
atom(s) of the [moleculetype] that >contains it, so if you only have one
[moleculetype] then any instance of it will have the restraint >applied
to whatever atoms are indicated.
-Justin
Hi Justin, thanks for your reply.
Craig Kitchen wrote:
Dear All,
My system consists of 32 identical molecules (with 91 atoms per
molecule). I would like to apply a position restraint to the 91st atom
of each molecules. Since all my molecules are identical I only have one
[moleculetype] which contains 91 atoms. I have defined
Dear All,
My system consists of 32 identical molecules (with 91 atoms per molecule).
I would like to apply a position restraint to the 91st atom of each
molecules. Since all my molecules are identical I only have one
[moleculetype] which contains 91 atoms. I have defined -DPOSRES in the .mdp
On 16/06/2011 11:54 AM, Tom Dupree wrote:
Greetings all,
I have run into a little bit of a problem.
I am trying to simulate a hetro-dimer. Through previous work we have identified
302 C-alphas (of 960 odd residues) that don't move much. Previously we
position restrained these atoms in our si
Greetings all,
I have run into a little bit of a problem.
I am trying to simulate a hetro-dimer. Through previous work we have identified
302 C-alphas (of 960 odd residues) that don't move much. Previously we
position restrained these atoms in our simulations using charmm which gave us a
sign
Mikhail Stukan wrote:
Dear gmx-users,
I am trying to simulate a thermalized wall in the framework of CG
Martini force field. To do this I am planning to link my wall atoms to
some reference points (initial positions) by harmonic potentials. From
what I have found in the manual it looks l
Dear gmx-users,
I am trying to simulate a thermalized wall in the framework of CG Martini force
field. To do this I am planning to link my wall atoms to some reference points
(initial positions) by harmonic potentials. From what I have found in the
manual it looks like this can be done by using
Since anybody helped me with this issue and I solved the problem, I'll
report the solution here to contribute with the comunity.
As I pointed in the original e-mail, the problem was the difference
between the numbering scheme of .gro file and .itp file.
I created 3 .pdb files, one for each ch
Hi all
I'm trying to simulate a system with 3 chains (A, H and L).
Pb2gmx gave me 3 .itp files (one for each chain), each one with atom
number starting from 1, and a .top file with these 3 .itp included. It
gave me also a .gro file with the 3 chains numbered consecutively (the
atom number
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Position Restraints
#ZHAO LINA# wrote:
> Thanks for your answer.
>
> How can I tell which ones I should restrain? all no-H atoms? in most general
> situations.
For the sake of clarity in the archive, it's probably be
ussion list for GROMACS users
Subject: Re: [gmx-users] Position Restraints
#ZHAO LINA# wrote:
Hi,
When I used the genrestr to get the posre.itp specially,
I found it set all atom to be applied to.
Is that okay? How could I figure out which ones should not be set to.
A little naive questions, but I
, September 22, 2010 11:15 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Position Restraints
#ZHAO LINA# wrote:
> Hi,
>
> When I used the genrestr to get the posre.itp specially,
> I found it set all atom to be applied to.
> Is that okay? How could I figure out wh
#ZHAO LINA# wrote:
Hi,
When I used the genrestr to get the posre.itp specially,
I found it set all atom to be applied to.
Is that okay? How could I figure out which ones should not be set to.
A little naive questions, but I do do not know.
The answer depends on your needs. When running ge
Hi,
When I used the genrestr to get the posre.itp specially,
I found it set all atom to be applied to.
Is that okay? How could I figure out which ones should not be set to.
A little naive questions, but I do do not know.
Thanks with regards,
lina
--
gmx-users mailing listgmx-users@gromacs
Jun 2010 09:43:18 -0400
> From: jalem...@vt.edu
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] position restraints
>
>
>
> abdullah ahmed wrote:
> > Hi!
> >
> > In your previous mail you mentioned:
> >
> > The position restraints m
and why.
Thank you again for your help,
Abdullah
> Date: Thu, 3 Jun 2010 09:43:18 -0400
> From: jalem...@vt.edu
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] position restraints
>
>
>
> abdullah ahmed wrote:
> > Hi!
> >
> > In your previous
abdullah ahmed wrote:
Hi!
In your previous mail you mentioned:
The position restraints must belong to the [moleculetype] of
the species to be restrained. * Once you #include a new molecule, you
start a new
[moleculetype] entry and the position restraints belong to it. *
So I rechecked my
Hi!
In your previous mail you mentioned:
The position restraints must belong to the [moleculetype] of
the species to be restrained. Once you #include a new molecule, you start a
new
[moleculetype] entry and the position restraints belong to it.
So I rechecked my .top file and found th
.org
> Subject: Re: [gmx-users] position restraints
>
>
>
> abdullah ahmed wrote:
> > Hello,
> >
> > I would like to restrain my molecule to a specific position in
space. I
> > would like for certain atoms to lie on the y-axis. To do
0 1000 ;
4 1 1000 0 1000 ;
5 1 1000 0 1000 ;
6 1 1000 0 1000 ;
7 1 1000 0 1000 ;
8 1 1000 0 1000 ;
9 1 1000 0 1000 ;
> Date: Thu, 3 Jun 2010 09:00:36 -0400
> From: jalem...@vt.edu
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] position restraints
>
>
>
&g
abdullah ahmed wrote:
Hello,
I would like to restrain my molecule to a specific position in space. I
would like for certain atoms to lie on the y-axis. To do this I used
the following code/lines in my .top file:
[ position restraints ]
This is an incorrect directive. It should be posit
Hello,
I would like to restrain my molecule to a specific position in space. I would
like for certain atoms to lie on the y-axis. To do this I used the following
code/lines in my .top file:
[ position restraints ]
2 1 1000 0 1000 ;
3 1 1000 0 1000 ;
4 1 1000 0 1000 ;
5 1 1000 0 1000 ;
6 1
[EMAIL PROTECTED] wrote:
Please ignore my previous mail. There was typo error.
Dear colleagues,
I want to do MD simulation of only the extracellular
domain of a pentamer, excluding the transmembrane domain. So, I want to
restrain the part of the extracellular domain in co
Please ignore my previous mail. There was typo error.
Dear colleagues,
I want to do MD simulation of only the extracellular
domain of a pentamer, excluding the transmembrane domain. So, I want to
restrain the part of the extracellular domain in contact with the
transmembrane
Dear colleagues,
I want to do MD simulation of only the extracellular domain
of a pentamer, excluding the transmembrane domain. So, I want to restrain the
part of the extracellular domain in contact with the transmembrane domain. I am
using "position restraints" for few of th
Quoting [EMAIL PROTECTED]:
> Hi,
>
> I minimized without restraints, could that be the problem?
> After the minimization I got a Potential Energy = -6.1434351e+02.
That seems fine. Basically, your lipid's headgroup is shearing itself apart
(which you can tell from the LINCS warnings). At this
Hi,
I minimized without restraints, could that be the problem?
After the minimization I got a Potential Energy = -6.1434351e+02.
Gadi
Quoting "Justin A. Lemkul" <[EMAIL PROTECTED]>:
Quoting [EMAIL PROTECTED]:
Hi,
The full mdrun output when the simulation blows up is:
Step 0, time 0 (ps)
Quoting chandrabhan seniya <[EMAIL PROTECTED]>:
> what is yr real prob tell me?
No need to get confrontational; my reply was not intended to be insulting. Mark
and I have been putting forth some effort to help our friend Gadi here by
extracting some detail that may be useful to document in the l
chandrabhan seniya wrote:
what is yr real prob tell me?
On this list, we like constructive criticism. I don't think the above
qualifies as such.
Mark
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what is yr real prob tell me?
On Thu, Apr 24, 2008 at 5:49 PM, Justin A. Lemkul <[EMAIL PROTECTED]> wrote:
> Quoting chandrabhan seniya <[EMAIL PROTECTED]>:
>
> > no prob you wait for some time it will write topology file and the
> proceed
> > further..
>
> I think that a lipid molecule trying t
Quoting chandrabhan seniya <[EMAIL PROTECTED]>:
> no prob you wait for some time it will write topology file and the proceed
> further..
I think that a lipid molecule trying to tear itself apart at step 0 would fall
under the category of a "problem," and it will not disappear on it's own if we
co
no prob you wait for some time it will write topology file and the proceed
further..
On Thu, Apr 24, 2008 at 5:04 PM, <[EMAIL PROTECTED]> wrote:
> Hi,
>
> The full mdrun output when the simulation blows up is:
>
> Step 0, time 0 (ps) LINCS WARNING
> relative constraint deviation after LINCS:
> m
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