[gmx-users] Speeding up g_angle calculations

[Igor Druz]

Hello,

Is there any way to speed up g_angle calculations ?

Thank you,
Igor
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[gmx-users] density

[mohammad agha]

Dear Prof. 


I have problems about density. I equilibrated my system consist 500 surfactants 
and 6 water molecules in martini coarse-grained for 120 ns and my results 
of g_energy next pr.mdp for density are:

average = 907.701
err.est = 0.61
rmsd = 2.54989
tot-drift = -3.4173

I don't know about good quantity of err.est, rmsd and tot-drift for density 
adjustment? and when my system has been equilibrated?
May I know about my problem, please?

On the other hand, "density distribution for different groups of the system in 
terms of their distance from micell's COM distance"  is considered In the 
articles about surfactants. I think that it is possible with g_density but this 
program compute the density as the function of  box(nm). May I know about this 
problem, Please?

Best Regards
sara
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Re: [gmx-users] Poor exchange probability for REMD

[David van der Spoel]

On 2011-11-20 03:03, ÏéÇ« ¿× wrote:

Dear Mark,
   Thanks for your prompt reply!

Pre-equilibration at the right temperature is always a good
idea, not just for REMD.


   Right temperature? I guess you mean pre-equilibrate at every replica 
temperatures, do you think so?


However for NVT REMD you need to
equilibrate the other temperatures at the same box size that
is sound for the temperature at which you want to make
observations.


   If i am interested in the properties at 3OOK, i may equilibrate the system 
at 300K with NPT ensemble, then equilibrate system at every replica 
temperatures with the same box size obtained from the NPT simulation at 300K.Is 
it right?

Why would you want to simulate at high pressure and high temperature? 
Your proteins will unfold even faster. NVT REMD means your replicas 
above 300 K will have too high P, at 360 K close to 1000 bar. Check 
http://folding.bmc.uu.se/remd/index.php if you need to choose T for 
REMD. The paper that describes the algorithm was published here: 
http://dx.doi.org/10.1039/b716554d



Even given that, there is no strong reason to suppose that
a temperature distribution following a simple mathematical
formula should lead to equal exchange probabilities on a
"real" system with free energy bottlenecks. Knowing that one
might need to be adding more replicas at relevant
temperatures is something that can only be determined
empirically - and probably from more than 2ns.


Yes, that's right! While the exchange probabilities were unequal for 
neighboring temperatures and maybe very high (0.3~0.4), i think i should remove 
some replicas at which the exchange probabilities were higher and add some 
replicas to increase the upper limit of the temperature range for REMD.
Meanwhile, anther question, what's the proper range for the exchange 
probability?  Does the high exchange probability impair the properties we want 
to observe or just a waste of computational resources?
Best regards!
Xiangqian Kong


--- On Sat, 11/19/11, Mark Abraham  wrote:


From: Mark Abraham
Subject: Re: [gmx-users] Poor exchange probability for REMD
To: "Discussion list for GROMACS users"
Date: Saturday, November 19, 2011, 12:14 AM
On 18/11/2011 12:43 PM, ÏéÇ« ¿×
wrote:

Dear GMX users，
  Recently i am performing the

REMD simulation with Gromacs program and the temperature
distribution for each replica was predicted with the server
"http://folding.bmc.uu.se/remd/";. However, after a 2-ns
short test simulation with 64 replicas  , i checked the
exchange probability for the neighboring replicas and find
the exchange probability was about 0.3 to 0.4 (as the file i
attached )but the desired probability was 0.2. Meanwhile, i
found the exchange probabilities fluctuated markedly for
each pair of  replicas while ideally we may hope they
were consistent with each other.  I don't know whether
this is acceptable or must be fixed up, or  a longer
simulation time and pre-equilibrium at different replica
temperature for each replica was needed.

Pre-equilibration at the right temperature is always a good
idea, not just for REMD. However for NVT REMD you need to
equilibrate the other temperatures at the same box size that
is sound for the temperature at which you want to make
observations.

Even given that, there is no strong reason to suppose that
a temperature distribution following a simple mathematical
formula should lead to equal exchange probabilities on a
"real" system with free energy bottlenecks. Knowing that one
might need to be adding more replicas at relevant
temperatures is something that can only be determined
empirically - and probably from more than 2ns.

Mark


   The system i simulated

includes 60074 atoms which consists of 155 residues,19173
waters and 14 chloridions. I first equilibrium the system
for 2ns with NPT ensemble at 300K, then start the REMD
simulation for 64 different replicas (temperature ranges
from 300 to 386K) with NVT ensemble and the exchange attempt
time was 2-ps(1000 integral steps).

   Now i was totally puzzled and

don't know how to figure out these problems,i am eager for
the help from you and any suggestions will be greatly
appreciated!

   Best regards!
   Xiangqian Kong


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--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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Re: [gmx-users] Poor exchange probability for REMD

[ÏéÇ« ¿×]

Dear Mark, 
  Thanks for your prompt reply!
> Pre-equilibration at the right temperature is always a good
> idea, not just for REMD. 

  Right temperature? I guess you mean pre-equilibrate at every replica 
temperatures, do you think so?

> However for NVT REMD you need to
> equilibrate the other temperatures at the same box size that
> is sound for the temperature at which you want to make
> observations.
  
  If i am interested in the properties at 3OOK, i may equilibrate the system at 
300K with NPT ensemble, then equilibrate system at every replica temperatures 
with the same box size obtained from the NPT simulation at 300K.Is it right?

> Even given that, there is no strong reason to suppose that
> a temperature distribution following a simple mathematical
> formula should lead to equal exchange probabilities on a
> "real" system with free energy bottlenecks. Knowing that one
> might need to be adding more replicas at relevant
> temperatures is something that can only be determined
> empirically - and probably from more than 2ns.

   Yes, that's right! While the exchange probabilities were unequal for 
neighboring temperatures and maybe very high (0.3~0.4), i think i should remove 
some replicas at which the exchange probabilities were higher and add some 
replicas to increase the upper limit of the temperature range for REMD. 
   Meanwhile, anther question, what's the proper range for the exchange 
probability?  Does the high exchange probability impair the properties we want 
to observe or just a waste of computational resources?
   Best regards!
   Xiangqian Kong
  

--- On Sat, 11/19/11, Mark Abraham  wrote:

> From: Mark Abraham 
> Subject: Re: [gmx-users] Poor exchange probability for REMD
> To: "Discussion list for GROMACS users" 
> Date: Saturday, November 19, 2011, 12:14 AM
> On 18/11/2011 12:43 PM, ÏéÇ« ¿×
> wrote:
> > Dear GMX users，
> >     Recently i am performing the
> REMD simulation with Gromacs program and the temperature
> distribution for each replica was predicted with the server
> "http://folding.bmc.uu.se/remd/";. However, after a 2-ns
> short test simulation with 64 replicas  , i checked the
> exchange probability for the neighboring replicas and find
> the exchange probability was about 0.3 to 0.4 (as the file i
> attached )but the desired probability was 0.2. Meanwhile, i
> found the exchange probabilities fluctuated markedly for
> each pair of  replicas while ideally we may hope they
> were consistent with each other.  I don't know whether
> this is acceptable or must be fixed up, or  a longer
> simulation time and pre-equilibrium at different replica
> temperature for each replica was needed.
> 
> Pre-equilibration at the right temperature is always a good
> idea, not just for REMD. However for NVT REMD you need to
> equilibrate the other temperatures at the same box size that
> is sound for the temperature at which you want to make
> observations.
> 
> Even given that, there is no strong reason to suppose that
> a temperature distribution following a simple mathematical
> formula should lead to equal exchange probabilities on a
> "real" system with free energy bottlenecks. Knowing that one
> might need to be adding more replicas at relevant
> temperatures is something that can only be determined
> empirically - and probably from more than 2ns.
> 
> Mark
> 
> >      The system i simulated 
> includes 60074 atoms which consists of 155 residues,19173
> waters and 14 chloridions. I first equilibrium the system
> for 2ns with NPT ensemble at 300K, then start the REMD
> simulation for 64 different replicas (temperature ranges
> from 300 to 386K) with NVT ensemble and the exchange attempt
> time was 2-ps(1000 integral steps).
> >      Now i was totally puzzled and
> don't know how to figure out these problems,i am eager for
> the help from you and any suggestions will be greatly
> appreciated!
> >      Best regards!
> >      Xiangqian Kong
> 
> -- gmx-users mailing list    gmx-users@gromacs.org
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[gmx-users] (no subject)

[Larif Sofiene]

Greeting
Is there a value from it we can be sure about hbond existence  in reality.
For example for a hbond occupancy rate of 10% we can say that this hbond has a 
good chance to exist in reality an effectively participate in the protein 
phenomena (movement,structure...) and for another hbond occupancy with 0.7% we 
can safely ignore it because it will not participate in protein behavior.
Is there such level value?-- 
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Re: [gmx-users] Protein Complex simulation

[Justin A. Lemkul]

Saba Ferdous wrote:
Dear Justin, 
I need to ask you that when we simulate 2 proteins and if the md.trr 
show both protein quite far then what can be inferred from this when the 
complex was simulated for 1ns.




If there was a protein complex at the outset of the simulation, you are probably 
observing a consequence of periodic boundary conditions.  1 ns is too short to 
observe anything useful, particularly a complete dissociation of a well-formed 
protein complex.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] Protein Complex simulation

[Saba Ferdous]

Dear Justin,
I need to ask you that when we simulate 2 proteins and if the md.trr show
both protein quite far then what can be inferred from this when the complex
was simulated for 1ns.

thanks with anticipation
Regards

-- 
Saba Ferdous
Research Scholar (M. Phil)
National Center for Bioinformatics
Quaid-e-Azam University, Islamabad
Pakistan
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Re: [gmx-users] Index file

[Justin A. Lemkul]

swati patel wrote:
Sorry,I did not realized about archive.Yess,It has solutions for many 
errors occuring in gromacs.


But the problem I am facing now is that i made index.idx file.Like in 
your tutorial i merged my protein and ligand group.


And the output is somewhat like this

 [ System ]
   123456789   10   11   12   13   14   15
  16   17   18   19   20

Only a series of numbers are there with no info of groups.

Please tell me how to make correct index file.



Please start by reading the manual.

-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] Index file

[swati patel]

Sorry,I did not realized about archive.Yess,It has solutions for many
errors occuring in gromacs.

But the problem I am facing now is that i made index.idx file.Like in your
tutorial i merged my protein and ligand group.

And the output is somewhat like this

 [ System ]
   123456789   10   11   12   13   14   15
  16   17   18   19   20

Only a series of numbers are there with no info of groups.

Please tell me how to make correct index file.

Thanx.
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Re: [gmx-users] (no subject)

[Justin A. Lemkul]

swati patel wrote:

Hello,

when executing this command g/_rompp -f pull.mdp -c npt.gro -p topol.top 
-n index.ndx -t npt.cpt -o pull.tpr
d  ,fatal error is giving that  "Group reference not found in 
indexfile._/"


Why am i getting this error??



You are calling a group named "reference" but no such group exists in the index 
file.  You need to create the group and add it to the index file.


Please also check the list archive when you get errors prior to posting.  Almost 
every error produced by a Gromacs program you will encounter has been asked and 
answered.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] (no subject)

[swati patel]

Hello,

when executing this command g*rompp -f pull.mdp -c npt.gro -p topol.top -n
index.ndx -t npt.cpt -o pull.tpr
d  ,fatal error is giving that  "Group reference not found in indexfile.*
"

Why am i getting this error??

Thanks.
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Re: [gmx-users] pull parameters

[Justin A. Lemkul]

ibi2010...@iiita.ac.in wrote:

Hello gmx_users,

I want to pull ligand out of binding pocket of protein using a spring of
some force constant which i will vary with each simulation and with
varying pulling velocity.

F=K(xspring - x ligand) using this equation.Now I am stucked up how to
decide initial position of ligand and spring i.e.afm_init1 and afm_vec.

Please guide me in this section.



I would suggest you upgrade to a more recent version of Gromacs and make use of 
the tutorial material available on the website.  Rather than use a Gromacs 
version from 5-6 years ago, a modern version (4.5.5) will give you better 
performance, newer features, greater stability, and significantly faster 
simulations.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] pull parameters

[ibi2010004]

Hello gmx_users,

I want to pull ligand out of binding pocket of protein using a spring of
some force constant which i will vary with each simulation and with
varying pulling velocity.

F=K(xspring - x ligand) using this equation.Now I am stucked up how to
decide initial position of ligand and spring i.e.afm_init1 and afm_vec.

Please guide me in this section.

Thanx.




-
This email has been sent using ArithMail at 
"Indian Institute of Information Technology, Allahabad, U.P, INDIA"
Web: http://www.iiita.ac.in, Email: cont...@iiita.ac.in

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Re: [gmx-users] g_wham error

[rajat desikan]

Oh lovely...thanks for the quick reply Justin :)...

On Sat, Nov 19, 2011 at 10:57 PM, Justin A. Lemkul  wrote:

>
>
> rajat desikan wrote:
>
>> Hi
>> I am a new gromacs user. I just completed Justin's umbrella sampling
>> tutorial. I am doing a PMF calculation between 2 methane molecules in
>> water. The simulation has run fine till the g_wham step. My command is
>>
>> -- g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal -b
>> 2000
>>
>> I get a warning:
>> WARNING, no data point in bin 2 (z=0.366256) !
>> You may not get a reasonable profile. Check your histograms!
>>
>> and my histogram contains a single peak.
>>
>> I have pulled my other methane 1 nm away from the first methane. I have
>> 15 sampling windows (0.05 nm apart till 5nm and then 1 nm apart)...can you
>> please tell me how to correct this?
>>
>>
> With 15 windows, you should have 15 histograms.  Plot with:
>
> xmgrace -nxy histo.xvg
>
> It will show you where the lack of sampling is.
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
> ==**==
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-- 
Rajat Desikan (Ph.D Scholar)
Prof. K. Ganapathy Ayappa's Lab (no 13),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore
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Re: [gmx-users] NVT simulation

[Justin A. Lemkul]

swati patel wrote:

hello Justin,

I am running NVT simulation for 20,000 steps.From last 40 minutes,It is 
showing on the screen NOTE: Turning on dynamic load balancing and no 
further steps are shown.Do generally NVT simulation takes a good amount 
of time or am I making a mistake somwhere in the parameter file?




I have no idea how long it should take, and the note does not indicate any 
problem.  The time for completion will depend upon a host of factors, not the 
least of which are the size of the system, number of available processors, 
neighbor searching frequency, and electrostatics method.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] NVT simulation

[swati patel]

hello Justin,

I am running NVT simulation for 20,000 steps.From last 40 minutes,It is
showing on the screen NOTE: Turning on dynamic load balancing and no
further steps are shown.Do generally NVT simulation takes a good amount of
time or am I making a mistake somwhere in the parameter file?

Thanx
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Re: [gmx-users] g_wham error

[Justin A. Lemkul]

rajat desikan wrote:

Hi
I am a new gromacs user. I just completed Justin's umbrella sampling 
tutorial. I am doing a PMF calculation between 2 methane molecules in 
water. The simulation has run fine till the g_wham step. My command is


-- g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal -b 2000

I get a warning:
WARNING, no data point in bin 2 (z=0.366256) !
You may not get a reasonable profile. Check your histograms!

and my histogram contains a single peak.

I have pulled my other methane 1 nm away from the first methane. I have 
15 sampling windows (0.05 nm apart till 5nm and then 1 nm apart)...can 
you please tell me how to correct this?




With 15 windows, you should have 15 histograms.  Plot with:

xmgrace -nxy histo.xvg

It will show you where the lack of sampling is.

-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] g_wham error

[rajat desikan]

Hi
I am a new gromacs user. I just completed Justin's umbrella sampling
tutorial. I am doing a PMF calculation between 2 methane molecules in
water. The simulation has run fine till the g_wham step. My command is

-- g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal -b 2000

I get a warning:
WARNING, no data point in bin 2 (z=0.366256) !
You may not get a reasonable profile. Check your histograms!

and my histogram contains a single peak.

I have pulled my other methane 1 nm away from the first methane. I have 15
sampling windows (0.05 nm apart till 5nm and then 1 nm apart)...can you
please tell me how to correct this?

Thanks

-- 
Rajat Desikan (Ph.D Scholar)
Prof. K. Ganapathy Ayappa's Lab (no 13),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore
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Re: [gmx-users] nvt equilibration

[Justin A. Lemkul]

swati patel wrote:

Hello Justin,

I am curious to know that why have nvt equilibration is not performed in 
umbrella sampling?




NVT is not necessarily required.  I just happen to know that the system used in 
the tutorial is rather robust and can proceed straight to NPT.  Typically NVT is 
advisable.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] nvt equilibration

[swati patel]

Hello Justin,

I am curious to know that why have nvt equilibration is not performed in
umbrella sampling?

Thanx.
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Re: [gmx-users] restraining the ligand.

[Justin A. Lemkul]

ibi2010...@iiita.ac.in wrote:

Hello gmx_users,

I have a query.I generated my ligand topology from swissparam using charmm
forcefields.Later in the tutorial after minimization step,You have
mentioned of program genrestr to restrain the ligand.

Is it applicable to all other methods that are not following prodrg
software.If not,then we have to change it directly in topology file?



The methodology in the tutorial can be applied to any system.  It is not 
PRODRG-specific and hopefully I have not given the impression that it should be.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] How to make coordinate file with correct numbering in the atoms when inbetween atoms are removed

[Justin A. Lemkul]

Ioannis Beis wrote:

Dear gromacs users,

It seems that because of my inexperience I have been trapped in a 
simple-looking labyrinth. I wanted to change a .gro file containing 
hydrated bilayer, in which I want to remove/modify certain atoms from 
certain lipid residues, e.g. cutting off a polar head. This kind of 
structure would serve as starting structure subject to equilibration. 
Since the resulting structures -after deleting certain atom lines- had 
atoms missing, the numbering in the .gro file was no longer correct. I 
tried using trjconv and trjcat to solve the problem and they were 
complaining about the inconsistency between total number of atoms and 
numbering. pdb2gmx was complaining about not finding my residues in the 
files of the forcefield, even though I explicitly gave as an input my 
topology.


I supposed that I could do the job in matlab. I wrote a script for the 
simplest case, which made the appropriate operations and saved the file 
exactly in the same format. Nevertheless, vmd could not visualize the 
file at all, even though grompp could use it as an input to assemble the 
binary .tpr . I tried fromdos with the .gro file but had no result. I 
also tried using trjconv on the "invisible" file with additional input 
the .tpr file that I made earlier and this produced a new .gro file with 
modified names for lipid residues (e.g. 1DOPC instead of first four 
digits of the name 1DOP as it was in the original file), but made the 
file visible by vmd. Nonetheless, vmd interpreted my modified lipid into 
two residues, i.e. one polar hydrogen as one and the rest lipid as 
another (??), despite the fact that the .gro file has the correct 
numbering of residues.


I know that some of the above problems might be independent, but all I 
am looking for eventually is if there is a practical implementation of 
typing five words and a program from the GROMACS package taking the n 
atoms of the .gro file and correcting their number ID into the correct 
one, based on the order they appear in the file, so that they become 
1,2,...,n without gaps.




Get a count of the number of atoms using 'wc -l' and subtract three - that's how 
many atoms you have.  Enter that on line 2 of the .gro file to make it a 
legitimate file.  Then:


genconf -renumber

-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] restraining the ligand.

[ibi2010004]

Hello gmx_users,

I have a query.I generated my ligand topology from swissparam using charmm
forcefields.Later in the tutorial after minimization step,You have
mentioned of program genrestr to restrain the ligand.

Is it applicable to all other methods that are not following prodrg
software.If not,then we have to change it directly in topology file?

Thanx.


-
This email has been sent using ArithMail at 
"Indian Institute of Information Technology, Allahabad, U.P, INDIA"
Web: http://www.iiita.ac.in, Email: cont...@iiita.ac.in

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[gmx-users] How to make coordinate file with correct numbering in the atoms when inbetween atoms are removed

[Ioannis Beis]

Dear gromacs users,

It seems that because of my inexperience I have been trapped in a  
simple-looking labyrinth. I wanted to change a .gro file containing  
hydrated bilayer, in which I want to remove/modify certain atoms from  
certain lipid residues, e.g. cutting off a polar head. This kind of  
structure would serve as starting structure subject to equilibration.  
Since the resulting structures -after deleting certain atom lines- had  
atoms missing, the numbering in the .gro file was no longer correct. I  
tried using trjconv and trjcat to solve the problem and they were  
complaining about the inconsistency between total number of atoms and  
numbering. pdb2gmx was complaining about not finding my residues in  
the files of the forcefield, even though I explicitly gave as an input  
my topology.


I supposed that I could do the job in matlab. I wrote a script for the  
simplest case, which made the appropriate operations and saved the  
file exactly in the same format. Nevertheless, vmd could not visualize  
the file at all, even though grompp could use it as an input to  
assemble the binary .tpr . I tried fromdos with the .gro file but had  
no result. I also tried using trjconv on the "invisible" file with  
additional input the .tpr file that I made earlier and this produced a  
new .gro file with modified names for lipid residues (e.g. 1DOPC  
instead of first four digits of the name 1DOP as it was in the  
original file), but made the file visible by vmd. Nonetheless, vmd  
interpreted my modified lipid into two residues, i.e. one polar  
hydrogen as one and the rest lipid as another (??), despite the fact  
that the .gro file has the correct numbering of residues.


I know that some of the above problems might be independent, but all I  
am looking for eventually is if there is a practical implementation of  
typing five words and a program from the GROMACS package taking the n  
atoms of the .gro file and correcting their number ID into the correct  
one, based on the order they appear in the file, so that they become  
1,2,...,n without gaps.


Thank you in advance.

Best regards,
Ioannis

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Re: [gmx-users] afm simulation

[Justin A. Lemkul]

I attempted to send this before, but received an error message from the list. 
Let's try again...


swati patel wrote:

Hello Justin,

I am following your tutorial on umbrella sampling.My project is on afm 
simulation of streptavidin-biotin complex.Till index.idx i ve created 
all my files.But as per your tutorial you have discussed of frames 
extraction and configurations.Since i am dealing with pull afm,so do I 
also need to extract frames and generate configuration ??


Yes.


Please tell me about the next step after doing npt equlibration and generating 
index.idx files?



Please follow the workflow of the tutorial.  If you are not clear on the 
underlying concepts, please spend some time in the literature.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] Fwd: afm simulation

[swati patel]

-- Forwarded message --
From: swati patel 
Date: Sat, Nov 19, 2011 at 3:18 PM
Subject: afm simulation
To: Discussion list for GROMACS users 


Hello Justin,

I am following your tutorial on umbrella sampling.My project is on afm
simulation of streptavidin-biotin complex.Till index.idx i ve created all
my files.But as per your tutorial you have discussed of frames extraction
and configurations.Since i am dealing with pull afm,so do I also need to
extract frames and generate configuration ??

Please tell me about the next step after doing npt equlibration and
generating index.idx files?

Thanx
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Re: [gmx-users] Reproducable MD runs on two PCs

[Mark Abraham]

On 19/11/2011 10:10 PM, Igor Druz wrote:

Hello,

I am running MDs on a linux PC with OpenSuse, using:

mpirun -np 4 mdrun -v -dlb auto -reprod 

If I repeat the calculation on the same PC, I get the same result. If 
I change to another PC with RedHat I get a different result.


Yep. http://www.gromacs.org/Documentation/Terminology/Reproducibility

More specifically, I am calculating a deviation from experiment, which 
varies by ~20 % on changing operating systems (pretty much the same 
hardware on both PCs). Is there any way to avoid such variations? I 
guess I am missing something in the mdp file, which is:


Change your gen_vel seed and I bet you observe a similar variation on 
the same machine. There are rather few systems that will have 
equilibrated in 2ns, never mind converged.


Mark



cpp =  /usr/bin/cpp -traditional
integrator   = sd
tinit= 0
dt   = 0.002
nsteps   = 100

nstcomm  = 1
nstcalcenergy= 1
nstxout  = 5
nstvout  = 100
nstlog   = 100
nstenergy= 100

nstlist  =  5
ns_type  = grid

pbc  = xyz
rlist= 0.9

optimize_fft = yes
coulombtype  = pme
rcoulomb = 0.9
epsilon-r= 1
rvdw = 0.9

constraints  = all-bonds
constraint-algorithm = Lincs

unconstrained-start  = yes
lincs-warnangle  = 30

tc_grps  = System
tau_t= 0.1
ref_t= 300.0

Pcoupl   = parrinello-rahman
tau_p= 2
compressibility = 4.5e-05
ref_p= 1.0

gen_vel  = yes
gen_temp = 300.0
gen_seed = 173529


Many thanks for your help,
Igor




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[gmx-users] Reproducable MD runs on two PCs

[Igor Druz]

Hello,

I am running MDs on a linux PC with OpenSuse, using:

mpirun -np 4 mdrun -v -dlb auto -reprod 

If I repeat the calculation on the same PC, I get the same result. If I
change to another PC with RedHat I get a different result. More
specifically, I am calculating a deviation from experiment, which varies by
~20 % on changing operating systems (pretty much the same hardware on both
PCs). Is there any way to avoid such variations? I guess I am missing
something in the mdp file, which is:

cpp =  /usr/bin/cpp -traditional
integrator   = sd
tinit= 0
dt   = 0.002
nsteps   = 100

nstcomm  = 1
nstcalcenergy= 1
nstxout  = 5
nstvout  = 100
nstlog   = 100
nstenergy= 100

nstlist  =  5
ns_type  = grid

pbc  = xyz
rlist= 0.9

optimize_fft = yes
coulombtype  = pme
rcoulomb = 0.9
epsilon-r= 1
rvdw = 0.9

constraints  = all-bonds
constraint-algorithm = Lincs

unconstrained-start  = yes
lincs-warnangle  = 30

tc_grps  = System
tau_t= 0.1
ref_t= 300.0

Pcoupl   = parrinello-rahman
tau_p= 2
compressibility = 4.5e-05
ref_p= 1.0

gen_vel  = yes
gen_temp = 300.0
gen_seed = 173529


Many thanks for your help,
Igor
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[gmx-users] afm simulation

[swati patel]

Hello Justin,

I am following your tutorial on umbrella sampling.My project is on afm
simulation of streptavidin-biotin complex.Till index.idx i ve created all
my files.But as per your tutorial you have discussed of frames extraction
and configurations.Since i am dealing with pull afm,so do I also need to
extract frames and generate configuration ??

Please tell me about the next step after doing npt equlibration and
generating index.idx files?

Thanx
-- 
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