Re: [gmx-users] Pressure stabilization during NPT phase

[Mark Abraham]

On 25/11/2011 6:53 PM, James Starlight wrote:
This way I've already used but is this possible to extract Gro and trp 
files from uncompleated runs and not stopping this simulation ?


Copy the trajectory file. Then use trjconv on the copy however suits 
you. You don't need a new .tpr, you need either the original .tpr or one 
that suits your analysis.


Mark




James

2011/11/25 Mark Abraham >


On 25/11/2011 6:38 PM, James Starlight wrote:

Mark, Tsjerk thanks!

I've check my uncompleated produced MD run by G_energy and find
that average pressure is 1.1 Bar that is most close to ref.


By the way could you tell me about extra possible ways of
checking running simmulation? ( E.g I'm calculating long produce
trajectory and want to check my uncompleated system ).

As I understood One of the possible way is the ussage of G_energy
but how I could obtain GRO and TPR file from uncompleated MD
trajectory ( .trr) (recently I've asked about this but I've
missed that topic ;o)  ?


Choose a length of time in advance that you are happy to risk
being wasted. Run that length of time, make a backup, check
whatever you want to check, then continue the simulation. As you
acquire confidence, you will want to increase that time (and like
everyone you will regret that decision at least once!)

Mark






Thanks again

James

2011/11/25 Tsjerk Wassenaar mailto:tsje...@gmail.com>>

Hi James,

There have been extensive discussions about this on the list.
Check the archives. In short, smaller systems give larger
fluctuations, and shorter simulations give larger deviations
from the expected average.

Cheers,

Tsjerk


On Nov 25, 2011 7:23 AM, "James Starlight"
mailto:jmsstarli...@gmail.com>> wrote:

Dear Gromacs Users!


At the present time I'm simulating small peptide (11 a.c in
coiled conformation) in water.

I've desided to use parameters from Lysozyme simmulation (
opls ff for parametrisation and all mdp parameters from that
simulation).

Because my peptide was smaller than typical globular protein
I've desided to use bigger periodical box than in tutorial

I've used editconf  -c -d 1.5 -bt cubic instead of 1.0 nm in
tutorial wich resulted in bigger box relative peptide size.

so i have this box vectors5.39318   5.39318   5.39318

My experiment was in full agreement with the above tutorial
until NVP phase was conducted. I have conducted 100ps
equilibration but When I've checked average pressure it was
0.75 atm instead of 1 BAR and have big RMSD- 200. (also I've
checked my system visually but it looks fine- I have not 
pointed any artifacts linked with unstable pressure like

voids in the solvent etc). Should I equilibrate my sustem
longer until pressure would not be stabilized to reference
BAR?  What another options should i take into account during
simulation of the small peptides ?

Thanks,

James

--
gmx-users mailing list gmx-users@gromacs.org

http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before
posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org
.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists


--
gmx-users mailing list gmx-users@gromacs.org

http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before
posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org
.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists







--
gmx-users mailing list gmx-users@gromacs.org

http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org
.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists






-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don

[gmx-users] grompp error

[yp sun]

Dear Sir'
 
When I ran the grompp as following
 
grompp -v -f md.mdp -c pr.gro -p RI-10.top -o md.tpr
 
a error information appeared: 
 

 
Program grompp, VERSION 3.3.1
Source code file: readir.c, line: 789
Fatal error:
Group Ptotein not found in indexfile
Maybe you have non-default goups in your mdp file, while not using the '-n' 
opti on of grompp.
In that case use the '-n' option
 
I don't know which file "Group Ptotein" is in and where I should make change.
 
Can you help me? Thanks in advance.

Yeping Sun
CAS Key Laboratory of Pathogenic Microbiology & Immunology
INSTITUTE OF MICROBIOLOGY CHINESE ACADEMY OF SCIENCES 
NO.1 Beichen West Road,Chaoyang District,Beijing 100101,china-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] grompp error

[Mark Abraham]

On 25/11/2011 7:09 PM, yp sun wrote:

Dear Sir'
When I ran the grompp as following
grompp -v -f md.mdp -c pr.gro -p RI-10.top -o md.tpr
a error information appeared:

Program grompp, VERSION 3.3.1
Source code file: readir.c, line: 789
Fatal error:
Group Ptotein not found in indexfile
Maybe you have non-default goups in your mdp file, while not using the 
'-n' opti on of grompp.

In that case use the '-n' option
I don't know which file "Group Ptotein" is in and where I should make 
change.

Can you help me? Thanks in advance.



You have referred to this group somewhere in your .mdp file, probably in 
error for "Protein". grompp went looking in the index file (possibly 
generated by default) and was confused when it didn't find what you told 
it was there to be found.


Mark
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] grompp error

[Gianluca Santoni]

The most reasonable thing is that there is a typo in your .mdp or in 
your .top files.

Check where you've written "Ptotein" instead of Protein


On 11/25/11 4:09 PM, yp sun wrote:

Dear Sir'
When I ran the grompp as following
grompp -v -f md.mdp -c pr.gro -p RI-10.top -o md.tpr
a error information appeared:

Program grompp, VERSION 3.3.1
Source code file: readir.c, line: 789
Fatal error:
Group Ptotein not found in indexfile
Maybe you have non-default goups in your mdp file, while not using the 
'-n' opti on of grompp.

In that case use the '-n' option
I don't know which file "Group Ptotein" is in and where I should make 
change.

Can you help me? Thanks in advance.

Yeping Sun
CAS Key Laboratory of Pathogenic Microbiology & Immunology
INSTITUTE OF MICROBIOLOGY CHINESE ACADEMY OF SCIENCES
NO.1 Beichen West Road,Chaoyang District,Beijing 100101,china






--
Gianluca Santoni,
Institut de Biologie Structurale
41 rue Horowitz
Grenoble
_
Please avoid sending me Word or PowerPoint attachments.
See http://www.gnu.org/philosophy/no-word-attachments.html

-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] calculating the pmf in constrained force simulations

[Ramya Parthasarathi]

Hi
I do constrained force simulations and i have the pullf.xvg and pullx.xvg
files.. I want to know how to calculate the force for each simulation and i
how to integrate the forces.. can some one help me.

Ramya
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] about relaxation protocol

[Albert]

Hi Tsjerk:

   I only found free energy calculation in the manual but there is 
nothing related to free energy pertubation stuff. Does anybody get 
related .mdp/scrips to do so ? I would like to relax my system very 
steadily.


THX
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] grompp error

[yp sun]

I think the same with you sir. But I just cann't find where I make this typing 
error of "Ptotein". I checked my md.mdp and RI-10.top and dind't find such a 
typo. Could you suggest any possible locations of this typo?

Yeping Sun
CAS Key Laboratory of Pathogenic Microbiology & Immunology
INSTITUTE OF MICROBIOLOGY CHINESE ACADEMY OF SCIENCES 
NO.1 Beichen West Road,Chaoyang District,Beijing 100101,china

--- 11年11月25日，周五, Gianluca Santoni  写道：


发件人: Gianluca Santoni 
主题: Re: [gmx-users] grompp error
收件人: "Discussion list for GROMACS users" 
日期: 2011年11月25日,周五,下午4:21



The most reasonable thing is that there is a typo in your .mdp or in your .top 
files.
Check where you've written "Ptotein" instead of Protein


On 11/25/11 4:09 PM, yp sun wrote: 





Dear Sir'
 
When I ran the grompp as following
 
grompp -v -f md.mdp -c pr.gro -p RI-10.top -o md.tpr
 
a error information appeared: 
 

 
Program grompp, VERSION 3.3.1
Source code file: readir.c, line: 789
Fatal error:
Group Ptotein not found in indexfile
Maybe you have non-default goups in your mdp file, while not using the '-n' 
opti on of grompp.
In that case use the '-n' option
 
I don't know which file "Group Ptotein" is in and where I should make change.
 
Can you help me? Thanks in advance.

Yeping Sun
CAS Key Laboratory of Pathogenic Microbiology & Immunology
INSTITUTE OF MICROBIOLOGY CHINESE ACADEMY OF SCIENCES 
NO.1 Beichen West Road,Chaoyang District,Beijing 100101,china

 


-- 
Gianluca Santoni,
Institut de Biologie Structurale
41 rue Horowitz
Grenoble
_
Please avoid sending me Word or PowerPoint attachments.
See http://www.gnu.org/philosophy/no-word-attachments.html
-下面为附件内容-


-- 
gmx-users mailing list    gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] grompp error

[yp sun]

Yes I find the in the mdp file I wrote "tc-grps=Ptotein Other". Sorry for this 
stupid error.
Thank you.

Yeping Sun
CAS Key Laboratory of Pathogenic Microbiology & Immunology
INSTITUTE OF MICROBIOLOGY CHINESE ACADEMY OF SCIENCES 
NO.1 Beichen West Road,Chaoyang District,Beijing 100101,china

--- 11年11月25日，周五, Gianluca Santoni  写道：


发件人: Gianluca Santoni 
主题: Re: [gmx-users] grompp error
收件人: "Discussion list for GROMACS users" 
日期: 2011年11月25日,周五,下午4:21



The most reasonable thing is that there is a typo in your .mdp or in your .top 
files.
Check where you've written "Ptotein" instead of Protein


On 11/25/11 4:09 PM, yp sun wrote: 





Dear Sir'
 
When I ran the grompp as following
 
grompp -v -f md.mdp -c pr.gro -p RI-10.top -o md.tpr
 
a error information appeared: 
 

 
Program grompp, VERSION 3.3.1
Source code file: readir.c, line: 789
Fatal error:
Group Ptotein not found in indexfile
Maybe you have non-default goups in your mdp file, while not using the '-n' 
opti on of grompp.
In that case use the '-n' option
 
I don't know which file "Group Ptotein" is in and where I should make change.
 
Can you help me? Thanks in advance.

Yeping Sun
CAS Key Laboratory of Pathogenic Microbiology & Immunology
INSTITUTE OF MICROBIOLOGY CHINESE ACADEMY OF SCIENCES 
NO.1 Beichen West Road,Chaoyang District,Beijing 100101,china

 


-- 
Gianluca Santoni,
Institut de Biologie Structurale
41 rue Horowitz
Grenoble
_
Please avoid sending me Word or PowerPoint attachments.
See http://www.gnu.org/philosophy/no-word-attachments.html
-下面为附件内容-


-- 
gmx-users mailing list    gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] vol in mdrun output

[Igor Druz]

"vol 0.63! imb F 25% pme/F 0.99 step 16389600..."

What does vol 0.63! stand for ?
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Pressure stabilization during NPT phase

[Tsjerk Wassenaar]

Hey,

You don't actually need to copy the trajectory. trjconv and other
tools are comfortable operating on an unfinished trajectory. They'll
just bail out at the end. As an alternative, here's a python one-liner
to extract the last frame (along with unfinished frames) from an XTC
trajectory:

python -c 'X=open("'$X'").read(); print X[X.rfind(X[:8]):]' > last.xtc

It will read in the whole trajectory in memory, so better not do it
with very large files ;)

Cheers,

Tsjerk

On Fri, Nov 25, 2011 at 9:08 AM, Mark Abraham  wrote:
> On 25/11/2011 6:53 PM, James Starlight wrote:
>
> This way I've already used but is this possible to extract Gro and trp files
> from uncompleated runs and not stopping this simulation ?
>
> Copy the trajectory file. Then use trjconv on the copy however suits you.
> You don't need a new .tpr, you need either the original .tpr or one that
> suits your analysis.
>
> Mark
>
>
>
> James
>
> 2011/11/25 Mark Abraham 
>>
>> On 25/11/2011 6:38 PM, James Starlight wrote:
>>
>> Mark, Tsjerk thanks!
>>
>> I've check my uncompleated produced MD run by G_energy and find that
>> average pressure is 1.1 Bar that is most close to ref.
>>
>>
>> By the way could you tell me about extra possible ways of checking running
>> simmulation? ( E.g I'm calculating long produce trajectory and want to check
>> my uncompleated system ).
>>
>> As I understood One of the possible way is the ussage of G_energy but how
>> I could obtain GRO and TPR file from uncompleated MD trajectory ( .trr)
>> (recently I've asked about this but I've missed that topic ;o)  ?
>>
>> Choose a length of time in advance that you are happy to risk being
>> wasted. Run that length of time, make a backup, check whatever you want to
>> check, then continue the simulation. As you acquire confidence, you will
>> want to increase that time (and like everyone you will regret that decision
>> at least once!)
>>
>> Mark
>>
>>
>>
>>
>> Thanks again
>>
>> James
>>
>> 2011/11/25 Tsjerk Wassenaar 
>>>
>>> Hi James,
>>>
>>> There have been extensive discussions about this on the list. Check the
>>> archives. In short, smaller systems give larger fluctuations, and shorter
>>> simulations give larger deviations from the expected average.
>>>
>>> Cheers,
>>>
>>> Tsjerk
>>>
>>> On Nov 25, 2011 7:23 AM, "James Starlight" 
>>> wrote:
>>>
>>> Dear Gromacs Users!
>>>
>>>
>>> At the present time I'm simulating small peptide (11 a.c in coiled
>>> conformation) in water.
>>>
>>> I've desided to use parameters from Lysozyme simmulation ( opls ff for
>>> parametrisation and all mdp parameters from that simulation).
>>>
>>> Because my peptide was smaller than typical globular protein I've desided
>>> to use bigger periodical box than in tutorial
>>>
>>> I've used editconf  -c -d 1.5 -bt cubic instead of 1.0 nm in tutorial
>>> wich resulted in bigger box relative peptide size.
>>>
>>> so i have this box vectors    5.39318   5.39318   5.39318
>>>
>>> My experiment was in full agreement with the above tutorial until NVP
>>> phase was conducted. I have conducted 100ps equilibration but When I've
>>> checked average pressure it was 0.75 atm instead of 1 BAR and have big RMSD-
>>> 200. (also I've checked my system visually but it looks fine- I have not
>>> pointed any artifacts linked with unstable pressure like voids in the
>>> solvent etc). Should I equilibrate my sustem longer until pressure would not
>>> be stabilized to reference BAR?  What another options should i take into
>>> account during simulation of the small peptides ?
>>>
>>> Thanks,
>>>
>>> James
>>>
>>> --
>>> gmx-users mailing list    gmx-users@gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>> Please don't post (un)subscribe requests to the list. Use the
>>> www interface or send it to gmx-users-requ...@gromacs.org.
>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> --
>>> gmx-users mailing list    gmx-users@gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>> Please don't post (un)subscribe requests to the list. Use the
>>> www interface or send it to gmx-users-requ...@gromacs.org.
>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>>
>>
>>
>>
>> --
>> gmx-users mailing list    gmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-requ...@gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
>
>
>
> --
> gmx-users mailing list    gmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/

Re: [gmx-users] multiple molecules simulations

[Tsjerk Wassenaar]

Hi Gloria,

It think it's pretty obvious that loose pieces will see one another
across periodic boundaries diffusing around the place. Whether it's a
good model of reality is something for you to verify. A priori, the
approach seems fine.

Cheers,

Tsjerk

On Fri, Nov 25, 2011 at 8:46 AM, Gloria Saracino  wrote:
> Dear all,
> I did not get an answer yet.
> I really want know your opinion.
> If you need other details about the simulation I'm willing to give it to
> you.
> Thank you in advance,
> Gloria
>
>
> 
> Da: Gloria Saracino 
> A: "gmx-users@gromacs.org" 
> Inviato: Giovedì 24 Novembre 2011 17:06
> Oggetto: [gmx-users] multiple molecules simulations
>
> Dear all,
> I have performed a simulation on eight identical peptides (composed by 11
> residues) embedded in explicit water. Box dimensions (cube of 7.92nm) have
> been chosen to get a high concentration to accelerate the aggregation
> process. PME has been used and rvdw=rcoulomb=0.9.
> The trajectory has been centered on a residue of a chain with
> trjconv -f *.xtc -center -pbc mol -s *.tpr -n *.ndx
> During the first 16ns even if each peptide cannot see its periodic image,
> the whole set of peptides (Protein in the index file) see itself in some
> frames at distances below 2nm, and in a very few of them below 0.9nm.
> Looking at the trajectory in vmd after less then 2ns I see the formation of
> an oligomer composed by six peptides, the other two peptides move around
> leaving the oligomer on a side and approaching on an other side. The
> oligomer never sees its periodic image as well as the two peptides never see
> their periodic image. The pi violations observed for the whole system
> correspond to the two peptides that, together or one at time, are placed
> between the oligomer and its pi. Considering 0.9nm as the distance below of
> which there is a direct interaction I found that when the minimum distance
> of the two peptides from one side of the oligomer is close to 0.9, the
> minimum distance from the other side is always above 1.4nm.
> Moreover the LJ and coulomb trends don't show abnormalities.
> Even if in simulations of a single molecule the effect of periodic image
> violation is a clear signal of a too small box to approximate a condition of
> infinite diluition, how I have to interpret such a violation for a system
> composed by multiple molecules and in which I want to reproduce a condition
> of high concentration?
> Can I use this simulation to study the behavior of the system at the chosen
> concentration?
> There are particular simulation settings or checks that I have to take into
> account to handle a high concentrated solution a
> nd that I overlooked?
>
> Any help will be appreciated (I apologize if some questions may seem
> trivial),
>
> Gloria
>
>
> --
> gmx-users mailing list    gmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
> --
> gmx-users mailing list    gmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Pressure stabilization during NPT phase

[Tsjerk Wassenaar]

Oh, I see I forgot to state that X should be set to the trajectory name:

X=/some/where/trajectory.xtc
python -c 'X=open("'$X'").read(); print X[X.rfind(X[:8]):]' > last.xtc

or just

python -c 'X=open("/some/where/trajectory.xtc").read(); print
X[X.rfind(X[:8]):]' > last.xtc

Cheers,

Tsjerk

On Fri, Nov 25, 2011 at 10:01 AM, Tsjerk Wassenaar  wrote:
> Hey,
>
> You don't actually need to copy the trajectory. trjconv and other
> tools are comfortable operating on an unfinished trajectory. They'll
> just bail out at the end. As an alternative, here's a python one-liner
> to extract the last frame (along with unfinished frames) from an XTC
> trajectory:
>
> python -c 'X=open("'$X'").read(); print X[X.rfind(X[:8]):]' > last.xtc
>
> It will read in the whole trajectory in memory, so better not do it
> with very large files ;)
>
> Cheers,
>
> Tsjerk
>
> On Fri, Nov 25, 2011 at 9:08 AM, Mark Abraham  wrote:
>> On 25/11/2011 6:53 PM, James Starlight wrote:
>>
>> This way I've already used but is this possible to extract Gro and trp files
>> from uncompleated runs and not stopping this simulation ?
>>
>> Copy the trajectory file. Then use trjconv on the copy however suits you.
>> You don't need a new .tpr, you need either the original .tpr or one that
>> suits your analysis.
>>
>> Mark
>>
>>
>>
>> James
>>
>> 2011/11/25 Mark Abraham 
>>>
>>> On 25/11/2011 6:38 PM, James Starlight wrote:
>>>
>>> Mark, Tsjerk thanks!
>>>
>>> I've check my uncompleated produced MD run by G_energy and find that
>>> average pressure is 1.1 Bar that is most close to ref.
>>>
>>>
>>> By the way could you tell me about extra possible ways of checking running
>>> simmulation? ( E.g I'm calculating long produce trajectory and want to check
>>> my uncompleated system ).
>>>
>>> As I understood One of the possible way is the ussage of G_energy but how
>>> I could obtain GRO and TPR file from uncompleated MD trajectory ( .trr)
>>> (recently I've asked about this but I've missed that topic ;o)  ?
>>>
>>> Choose a length of time in advance that you are happy to risk being
>>> wasted. Run that length of time, make a backup, check whatever you want to
>>> check, then continue the simulation. As you acquire confidence, you will
>>> want to increase that time (and like everyone you will regret that decision
>>> at least once!)
>>>
>>> Mark
>>>
>>>
>>>
>>>
>>> Thanks again
>>>
>>> James
>>>
>>> 2011/11/25 Tsjerk Wassenaar 

 Hi James,

 There have been extensive discussions about this on the list. Check the
 archives. In short, smaller systems give larger fluctuations, and shorter
 simulations give larger deviations from the expected average.

 Cheers,

 Tsjerk

 On Nov 25, 2011 7:23 AM, "James Starlight" 
 wrote:

 Dear Gromacs Users!


 At the present time I'm simulating small peptide (11 a.c in coiled
 conformation) in water.

 I've desided to use parameters from Lysozyme simmulation ( opls ff for
 parametrisation and all mdp parameters from that simulation).

 Because my peptide was smaller than typical globular protein I've desided
 to use bigger periodical box than in tutorial

 I've used editconf  -c -d 1.5 -bt cubic instead of 1.0 nm in tutorial
 wich resulted in bigger box relative peptide size.

 so i have this box vectors    5.39318   5.39318   5.39318

 My experiment was in full agreement with the above tutorial until NVP
 phase was conducted. I have conducted 100ps equilibration but When I've
 checked average pressure it was 0.75 atm instead of 1 BAR and have big 
 RMSD-
 200. (also I've checked my system visually but it looks fine- I have not
 pointed any artifacts linked with unstable pressure like voids in the
 solvent etc). Should I equilibrate my sustem longer until pressure would 
 not
 be stabilized to reference BAR?  What another options should i take into
 account during simulation of the small peptides ?

 Thanks,

 James

 --
 gmx-users mailing list    gmx-users@gromacs.org
 http://lists.gromacs.org/mailman/listinfo/gmx-users
 Please search the archive at
 http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
 Please don't post (un)subscribe requests to the list. Use the
 www interface or send it to gmx-users-requ...@gromacs.org.
 Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

 --
 gmx-users mailing list    gmx-users@gromacs.org
 http://lists.gromacs.org/mailman/listinfo/gmx-users
 Please search the archive at
 http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
 Please don't post (un)subscribe requests to the list. Use the
 www interface or send it to gmx-users-requ...@gromacs.org.
 Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>>
>>>
>>>
>>>
>>> --
>>> gmx-users mailing list    gmx-users@gromacs.org
>>> http://l

Re: [gmx-users] multiple molecules simulations

[Gloria Saracino]

Thank you Tsjerk, this is encouraging for me!

Gloria





 Da: Tsjerk Wassenaar 
A: Gloria Saracino ; Discussion list for GROMACS users 
 
Inviato: Venerdì 25 Novembre 2011 10:10
Oggetto: Re: [gmx-users] multiple molecules simulations
 
Hi Gloria,

It think it's pretty obvious that loose pieces will see one another
across periodic boundaries diffusing around the place. Whether it's a
good model of reality is something for you to verify. A priori, the
approach seems fine.

Cheers,

Tsjerk

On Fri, Nov 25, 2011 at 8:46 AM, Gloria Saracino  wrote:
> Dear all,
> I did not get an answer yet.
> I really want know your opinion.
> If you need other details about the simulation I'm willing to give it to
> you.
> Thank you in advance,
> Gloria
>
>
> 
> Da: Gloria Saracino 
> A: "gmx-users@gromacs.org" 
> Inviato: Giovedì 24 Novembre 2011 17:06
> Oggetto: [gmx-users] multiple molecules simulations
>
> Dear all,
> I have performed a simulation on eight identical peptides (composed by 11
> residues) embedded in explicit water. Box dimensions (cube of 7.92nm) have
> been chosen to get a high concentration to accelerate the aggregation
> process. PME has been used and rvdw=rcoulomb=0.9.
> The trajectory has been centered on a residue of a chain with
> trjconv -f *.xtc -center -pbc mol -s *.tpr -n *.ndx
> During the first 16ns even if each peptide cannot see its periodic image,
> the whole set of peptides (Protein in the index file) see itself in some
> frames at distances below 2nm, and in a very few of them below 0.9nm.
> Looking at the trajectory in vmd after less then 2ns I see the formation of
> an oligomer composed by six peptides, the other two peptides move around
> leaving the oligomer on a side and approaching on an other side. The
> oligomer never sees its periodic image as well as the two peptides never see
> their periodic image. The pi violations observed for the whole system
> correspond to the two peptides that, together or one at time, are placed
> between the oligomer and its pi. Considering 0.9nm as the distance below of
> which there is a direct interaction I found that when the minimum distance
> of the two peptides from one side of the oligomer is close to 0.9, the
> minimum distance from the other side is always above 1.4nm.
> Moreover the LJ and coulomb trends don't show abnormalities.
> Even if in simulations of a single molecule the effect of periodic image
> violation is a clear signal of a too small box to approximate a condition of
> infinite diluition, how I have to interpret such a violation for a system
> composed by multiple molecules and in which I want to reproduce a condition
> of high concentration?
> Can I use this simulation to study the behavior of the system at the chosen
> concentration?
> There are particular simulation settings or checks that I have to take into
> account to handle a high concentrated solution a
> nd that I overlooked?
>
> Any help will be appreciated (I apologize if some questions may seem
> trivial),
>
> Gloria
>
>
> --
> gmx-users mailing list    gmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
> --
> gmx-users mailing list    gmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] QM/MM energies

[Jon Mujika]

Dear gmx users,

I am performing some QM/MM optimizations using the ORCA interface in
order to compare the energies of different structures of the same
system. However, I have some questions related with the energy terms.

In the output file the "potential" and "Quantum Ener." terms are
printed out. The question is: does the Potential term include the QM
energy? That is, is the "potential" energy the total QM/MM energy, or
only the MM part of the total energy? On the other hand, since I am
using the electronic embedding approach (QMMMscheme=normal in the .mdp
file), I assume that the QM/MM electrostatic energy is included in the
QM term. Is that correct? And what about the QM/MM van der Waals
energy?

I ask so because I try to calculate the potential energy from the
different terms provided in the output, but I can't reproduce the
potential energy.

Thanks for you help

Jon
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] Re: gmx-users Digest, Vol 91, Issue 184

[Sławomir Stachura]

Miło mi to słyszeć. W takim razie czekam na przesyłkę.
Pozdrawiam, 
Sławomir Stachura


Wiadomość napisana przez gmx-users-requ...@gromacs.org w dniu 2011-11-25, o 
godz. 12:00:

> Send gmx-users mailing list submissions to
>   gmx-users@gromacs.org
> 
> To subscribe or unsubscribe via the World Wide Web, visit
>   http://lists.gromacs.org/mailman/listinfo/gmx-users
> or, via email, send a message with subject or body 'help' to
>   gmx-users-requ...@gromacs.org
> 
> You can reach the person managing the list at
>   gmx-users-ow...@gromacs.org
> 
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of gmx-users digest..."
> 
> 
> Today's Topics:
> 
>   1. QM/MM energies (Jon Mujika)
> 
> 
> --
> 
> Message: 1
> Date: Fri, 25 Nov 2011 11:08:34 +0100
> From: Jon Mujika 
> Subject: [gmx-users] QM/MM energies
> To: gmx-users@gromacs.org
> Message-ID:
>   
> Content-Type: text/plain; charset=ISO-8859-1
> 
> Dear gmx users,
> 
> I am performing some QM/MM optimizations using the ORCA interface in
> order to compare the energies of different structures of the same
> system. However, I have some questions related with the energy terms.
> 
> In the output file the "potential" and "Quantum Ener." terms are
> printed out. The question is: does the Potential term include the QM
> energy? That is, is the "potential" energy the total QM/MM energy, or
> only the MM part of the total energy? On the other hand, since I am
> using the electronic embedding approach (QMMMscheme=normal in the .mdp
> file), I assume that the QM/MM electrostatic energy is included in the
> QM term. Is that correct? And what about the QM/MM van der Waals
> energy?
> 
> I ask so because I try to calculate the potential energy from the
> different terms provided in the output, but I can't reproduce the
> potential energy.
> 
> Thanks for you help
> 
> Jon
> 
> 
> --
> 
> -- 
> gmx-users mailing list
> gmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> 
> End of gmx-users Digest, Vol 91, Issue 184
> **

--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] q4md-forcefieldtools.org announcement

[FyD]

Dear All,

I am pleased to announce the official release of the latest  
developments at http://q4md-forcefieldtools.org.


q4md-forcefieldtools.org regroups an ensemble of tools, server,  
database and tutorials related to empirical force field developments.  
Theses developments are designed for the AMBER and GLYCAM force  
fields, but can also have applications in CHARMM and OPLS force field  
based simulations.


At the basis of our work is the RESP and ESP charge Derive (R.E.D.)  
program devoted to RESP and ESP charge derivation and force field  
library building for new molecules and potentially any type of  
molecular fragments. The approach leads to reproducible charge values  
independently of the quantum chemistry program interfaced or initial  
structure chosen by the user. In complex approaches, multiple  
molecules, multiple conformations and multiple orientations are  
involved in charge derivation and force field library building, and a  
large set of force field libraries or Force Field Topology DataBase  
(FFTopDB) is generated. The procedure is now compatible with any type  
of biomolecules and bioinorganic molecules (nucleic acids, proteins,  
glycoconjugates, organic and bioinorganic structures in the ground or  
excited states; covalently or non-covalently bound; natural structures  
as well as chemically engineered or artificial analogs).


. The standalone version of the R.E.D. tools is available at  
http://q4md-forcefieldtools.org/RED/.
. R.E.D. Server available at http://q4md-forcefieldtools.org/REDS/ is  
a Web server, which provides all required software and hardware for  
charge derivation and force field library building. It interfaces the  
latest versions of the Ante_R.E.D. and R.E.D. programs.
. R.E.DD.B. is a database of RESP and ESP charges and force field  
libraries available at http://q4md-forcefieldtools.org/REDDB/.

. Related tutorials are at http://q4md-forcefieldtools.org/Tutorial/.


* New web tools have been developed in R.E.D. Server allowing the  
automatic and simultaneous generation of force field libraries for the  
nucleotide or amino-acid fragments.
. N-terminal, C-terminal and central fragments for a new amino-acid  
residue from a single dipeptide

 http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#25
. 5'-terminal, 3'-terminal and central fragments for a new nucleotide  
residue from a single nucleoside

 http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#27

* A new R.E.D. Server version named "R.E.D. Server Development" has  
been developed.
R.E.D. Server Development allows RESP and ESP charge derivation and  
force field library building for new molecules and fragments involving  
all the elements of the periodic table. Several user defined options  
have been also incorporated in this server.

 See http://q4md-forcefieldtools.org/REDS-Development/
 http://q4md-forcefieldtools.org/REDS-Development/faq.php
 http://q4md-forcefieldtools.org/REDS-Development/faq.php#17

* New R.E.DD.B. features have been developed representing the first  
step toward R.E.DD.B. 2.0, a database of Force Field Topology DataBase.
 New scripts have been written allowing the automatic submission in  
R.E.DD.B. of data generated by the R.E.D. tools and R.E.D. Server.

 See http://q4md-forcefieldtools.org/REDDB/faq.php#5
 PubMed ID indexation is now incorporated in R.E.DD.B.
 New Force Field Topology DataBases are available. Among others see  
representative examples:

 http://q4md-forcefieldtools.org/REDDB/projects/F-88/
 http://q4md-forcefieldtools.org/REDDB/projects/F-87/
 http://q4md-forcefieldtools.org/REDDB/projects/F-85/

* A new force field library file format has been developed within the  
LEaP program (AmberTools 1.5).
 The mol3 force field library file format was developed. This file  
format merge some advantages of the Tripos mol2 and AMBER OFF file  
formats within t/xLEaP.

 See http://q4md-forcefieldtools.org/Tutorial/leap-mol3.php

* Updated RESP version 2.2 for charge fitting for metal complexes and  
large set of molecules, conformations and orientations.

 See http://q4md-forcefieldtools.org/RED/resp/

* Tutorials have been updated accordingly to these new features.

* The articles describing R.E.DD.B., R.E.D. and R.E.D. Server are all  
freely available under the following PubMed Central reference number:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2238896/
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2918240/
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125739/


All our tools and data are open to all, and are in agreement with the  
GNU General Public License 3.0.


regards, Francois


  F.-Y. Dupradeau
---
http://q4md-forcefieldtools.org/FyD/

--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the li

[gmx-users] making movie from trajectories

[Saman Mandegar]

Dear All,

I would like to make a movie from my trajectories using vmd. I need to make a 
movie which during the simulation the color of model is changing after some 
frames during the dynamics (showing
the transition between two states), this is accompanied by showing the change 
in time clock and the annotation (title) on the movie.  I am working on a 
script to add the time clock to simulations animations by modifying the pov 
files.
Could anybody please tell me how I can do that? or possibly share his/her 
script with me?

I appreciate your reply in advance.
Best wishes,
Saman
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] translational diffusion of the water at the micelle surface

[intra\sa175950]

Hi everybody, 

 

I would like to compute the translational diffusion around the micelle
surface. I know that I can select the water molecules at x distance of the
micelle surface with g_select (right ?) but how to use this file generated
by g_select to compute de diffusion, since the index and/or the number of
water will change with the simulation time . 

 

Thank you for your response 

 

Stephane 

-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] QM/MM energies

[Christoph Riplinger]

Dear Jon,

To the best of my knowledge the potential energy is the sum of all 
energies (E_QM + E_MM + E_QM/MM). The quantum energy (actually I do not 
see it in my output) for electrostatic embedding includes E_QM + 
E_QM/MM(el.stat.). I.e. E_QM/MM(VDW) you have to extract from the edr 
file. You should have two different energy groups, one defining the QM, 
and the other one defining the remaining system. I.e. you can extract 
E_QM/MM(VDW) from the sum of LJ-SR:notQM-QM and LJ-14:notQM-QM.


Importantly, if you want to analyze the QM_part of the energy, you 
should (i) either calculate E_QM without the point charges again, or 
(ii) add E_QM/MM(VDW) to the printed quantum energy (i.e. calculate E_QM 
+ E_QM/MM), since the electrostatic QM/MM contribution is included in 
the quantum energy for electrostatic embedding, and it is highly 
dependent on the  respective VDW contribution.


Hope that helps,
Christoph Riplinger



On 11/25/2011 11:08 AM, Jon Mujika wrote:

Dear gmx users,

I am performing some QM/MM optimizations using the ORCA interface in
order to compare the energies of different structures of the same
system. However, I have some questions related with the energy terms.

In the output file the "potential" and "Quantum Ener." terms are
printed out. The question is: does the Potential term include the QM
energy? That is, is the "potential" energy the total QM/MM energy, or
only the MM part of the total energy? On the other hand, since I am
using the electronic embedding approach (QMMMscheme=normal in the .mdp
file), I assume that the QM/MM electrostatic energy is included in the
QM term. Is that correct? And what about the QM/MM van der Waals
energy?

I ask so because I try to calculate the potential energy from the
different terms provided in the output, but I can't reproduce the
potential energy.

Thanks for you help

Jon


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] making movie from trajectories

[Mark Abraham]

On 26/11/2011 1:55 AM, Saman Mandegar wrote:

Dear All,

I would like to make a movie from my trajectories using vmd. I need to 
make a movie which during the simulation the color of model is 
changing after some frames during the dynamics (showing
the transition between two states), this is accompanied by showing the 
change in time clock and the annotation (title) on the movie.  I am 
working on a script to add the time clock to simulations animations by 
modifying the pov files.
Could anybody please tell me how I can do that? or possibly share 
his/her script with me?


This procedure is outside the scope of GROMACS. I suggest you search the 
VMD resources and enquire on the VMD mailing list.


Mark
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] NVT Equilibration

[Alex Jemulin]

Dear all
I'm studying a membrane protein. I've run equilibration with the follwing 
parameters - reference temperature =323k
integrator = md  ; leap-frog integrator
nsteps  = 5  ; 2 * 5 = 100 ps
dt  = 0.002  ; 2 fs
tcoupl  = V-rescale ; modified Berendsen thermostat
The system converged quickly to the reference value (after 2-3ps).
Should it converge more slowly and gradually? In the case how could fix it?
Thanks-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists