Re: [gmx-users] regarding simulation of peptide and protein complex

[Javier Cerezo]

  
  
Hi Rashi

To me, it seems more reasonable to use "pdb2gmx" for every molecule
that is supported by this utility (i.e. included in a rtp file) as
it will be more likely to be FF-compliant (at least for the default
rtp files) and thus compatible with your protein. PRODRG is, used
with some cautions, a very nice tool for kind of non-standard
ligands (as drugs) not included is such databases, but just for
them. 

If the starting PDB structure of your peptide is OK you would be
able to run "pdb2gmx" properly. Just try it and see

Javier


El 14/07/11 08:39, rashi parihar escribió:
Hello everyone..
  I have to do the simulation of protein and peptide complex.I want
  to ask as for protein and ligand complex we have to create
  topology of ligand using prodrg sever mostly.Now if ligand is
  peptide then I have to build the topology of  peptide using
  pdb2gx  or anyother means?Looking forward 4r reply!! 
  
  -- 
   
  
   
  “Many Smiles Begin Because Of Another Smile . . . ." 
 
Regards,
Rashi
  


  

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Re: [gmx-users] Residence time and trjorder

[Chandan Choudhury]

Hi gmx-users,

I tried installing the tool, g_residence.c

I am using gromacs-4.0.7
I copied it to the src/tools. There, I executed make command

# make g_residence

cc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused
-funroll-all-loops -I/opt/fftw-3.2.2/include -L/opt/fftw-3.2.2/lib
g_residence.c   -o g_residence
g_residence.c:42:22: fatal error: sysstuff.h: No such file or directory
compilation terminated.
make: *** [g_residence] Error 1

How do the tool can be installed?

Chandan

--
Chandan kumar Choudhury
NCL, Pune
INDIA


On Wed, Jul 13, 2011 at 8:24 PM, XAvier Periole  wrote:

>
> Mark is right g_dist can help you for this but there is no specific
> tool calculating residence time ... I guess everyone dreams of
> someone writing it :))
>
> On Jul 13, 2011, at 2:28 AM, Mark Abraham wrote:
>
>  On 13/07/2011 5:52 PM, Carla Jamous wrote:
>
> Dear Xavier,
>
> my problem is the following:
>
> I'm trying to figure out if a water molecule is present in a specific area
> around my protein and if so, which water molecule is that and how long does
> it stay in that place.
>
>
> I think g_dist does this for a group containing a single water molecule.
> All you need to do write a script to iterate over each molecule, and then
> collate the statistics.
>
> Mark
>
> As you said, if I google residence time, here's the definition: *Residence
> time* (also known as *removal time*) is the average amount of time that a
> particle  spends in a particular
> system.
>
> But I don't find a tool to calculate this residence time in gromacs, so I'm
> trying to find a trick that can give me a pourcentage of the time of my
> simulation where a certain water molecule stays in the specific area of my
> protein.
>
> Regards,
> Carla
>
> On Tue, Jul 12, 2011 at 5:51 PM, XAvier Periole  wrote:
>
>>
>> Dear Boafu,
>>
>> This sounds like a great tool!
>>
>> Carla, note that once you've ordered the water molecules you loose
>> the continuity of their trajectories ... that is because you order them in
>> function of their distance to the protein.
>>
>> I am not sure the definition you give will give you the answer to the
>> residence time. you can google residence time and proteins and see
>> what come out :))
>>
>> XAvier.
>>
>>
>> On Jul 12, 2011, at 6:32 AM, Baofu Qiao wrote:
>>
>>HI Carla,
>>>
>>> I wrote a similar code, see attached. But it is written for my condition.
>>> You should modify it accordingly.
>>>
>>> regards,
>>> Baofu Qiao
>>>
>>> On 07/12/2011 02:04 PM, Carla Jamous wrote:
>>>
 Dear gmx-users,

 I used trjorder in order to study the water molecules that are closer
 than 5 A from my protein.

 trjorder -s structure.tpr -f traj.xtc -n prot_water.ndx -o ordered.pdb
 -nshell nshell_.xvg -r 0.5 -b 0 -e 5000

 But now I need to analyse the residence time of a water molecule, I mean
 the number of times a single water molecule stays in a radius of 5 A of the
 protein and divide this number by the total number of conformations, in
 order to have a pourcentage value.

 Please is there any gromacs tool able to do this calculation or else
 does anyone have an idea of how to do that?

 Thank you

 Carla

>>>
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>>
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[gmx-users] Regarding phenyl rings absolutely flat.

[HARESH AJANI]

Hello Dear,

I am using gromacs 4.5.3 version. 

I am doing simulation of Protein-Ligand complex. My all system is right but I have confusion related to Planarity aromatic ring.

My ligand have 3 aromatics ring. 

I have generated .itp file from Prodrg and i have setup very well.

My ligand planer/flat(3  phenyl ring) during EM/NVT/NPT but after given mdrun I have given for 10 ns.

I have dump pdb file at 1ns but my ligand lost planer structure.

I have lot of question related to Ligand and Protein ?

1. Have any problem with protein-ligand H-bond interaction ?
2. As per chemistry aromatics structure should have remain planer ?
3. Any problem with simulation ?
4. sily question- If aromatics structure bent then any problem with Protein-ligand interaction/ Binding site  ?

Hope I will get best answer.

Thanks In advance  
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Re: [gmx-users] maintained an Hbond using a distance restraint

[Mark Abraham]

On 14/07/2011 11:28 AM, Itamar Kass wrote:

Hi,

I wish to force my system to maintained an Hbond during a simulation. 
In order to do so I am using a distance restraint protocol, with the 
following parameters:


In the topology file/:

/[ distance_restraints ]
; ai aj type index type' low up1 up2 fac
  2786 3262 10 2 0.295 0.305 0.315 1.0 ;

and in the run input file:

; DISTANCE RESTRAINTS
disre   =  simple
disre_weighting =  equal
disre_fc=  20
disre_mixed =  yes
disre_tau   =  10
nstdisreout =  1000

The atoms numbering was taken from the topology file ( /268LYSHNZ 
2786   3.939   7.037   5.060  0.2307 -0.0416 -0.3125/ and /320GLU
OE1 3262   3.872   6.806   4.875 -0.2077 -0.0055 -0.1229/ ) and is 
based the crystal structure (for atoms and distance).


Those lines are from .gro files, not topology files. 
[distance_restraints] are specific to a [moleculetype], and must use the 
atom indices established in the [atoms] section of the [moleculetype]. 
Anything found in a .gro file is irrelevant, but might be fortuitously 
accurate.


Mark


When I looked into the tpr file, the same atoms are numbered differently.

My questions are:
1. should I use the numbering as given in the topology file?
2. Am I using it correctly? Should I use a force bigger then 20kJ?

All the best,
Itamar

PS I am using GROMACS VERSION 4.0.7 in double precisin on a Linux cluster.
--


"In theory, there is no difference between theory and practice. But, in practice, 
there is." - Jan L.A. van de Snepscheut

===
| Itamar Kass, Ph.D.
| Postdoctoral Research Fellow
|
| Department of Biochemistry and Molecular Biology
| Building 77 Clayton Campus
| Wellington Road
| Monash University,
| Victoria 3800
| Australia
|
| Tel: +61 3 9902 9376
| Fax: +61 3 9902 9500
| E-mail:itamar.k...@monash.edu



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Re: [gmx-users] Regarding phenyl rings absolutely flat.

[Mark Abraham]

On 14/07/2011 5:50 PM, HARESH AJANI wrote:
Hello Dear, I am using gromacs 4.5.3 version. I am doing simulation of 
Protein-Ligand complex. My all system is right but I have confusion 
related to Planarity aromatic ring. My ligand have 3 aromatics ring. I 
have generated .itp file from Prodrg and i have setup very well. My 
ligand planer/flat(3 phenyl ring) during EM/NVT/NPT but after given 
mdrun I have given for 10 ns. I have dump pdb file at 1ns but my 
ligand lost planer structure.


Probably your topology lacks the improper dihedrals (see manual) used to 
preserve planarity in such cases. You should read the PRODRG 
documentation about how it handles such cases.


I have lot of question related to Ligand and Protein ? 1. Have any 
problem with protein-ligand H-bond interaction ? 


Don't know what you mean.

2. As per chemistry aromatics structure should have remain planer ? 


Yes.

3. Any problem with simulation ? 


Certainly.

4. sily question- If aromatics structure bent then any problem with 
Protein-ligand interaction/ Binding site ? 


It doesn't model reality, so yes, there's a problem.

Mark

Hope I will get best answer. Thanks In advance 


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[gmx-users] Force components on ATOM XX

[nahren manuel]

Dear Gromacs Users,
Is it possible to get the forces (components, x,y, z) acting on each atom from 
the simulation  or from the rerun. 

I need them to calculate the Hessian
Similar to 

http://www.sciencedirect.com/science/article/pii/S0006349507715989

Best,

nahren
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Re: [gmx-users] REMD with 'bad contacts' error

[Sheeba Jem]

Hi, I had been trying different thermostats, barostats, time steps and
coupling times to get remd for the peptide lipid system working and I had
even equilibrated each replica for 50 ns before submitting them to remd.
However none of them work when I use one processor per replica. That is, I
have 50 replicas and when I submit the job with 50 processors the job
crashes with the bad contacts error. However when I use 4 processors per
replica that is 200 processors instead of 50 then the job runs fine without
any problem.

So I went back to the equilibrated systems described in my first mail and
used the nose hoover thermostat, parinello-rahman semi-isotropic pressure
coupling, coupled the protein, lipid, water and ions separately with no
velocity generation and used 4 processors per replica and the simulation
runs fine. I had ran a 20 ns remd run and it has completed successfully but
for the exact same tpr files when I use 1 processor per replica I get the
bad contacts error. Could the remd crashing have been due to some scaling
issue? if so, the error in the log files with 'bad contacts' was
misleading...

Sheeba





On Wed, Jul 6, 2011 at 1:06 AM, Mark Abraham wrote:

> **
> On 6/07/2011 2:49 PM, Sheeba Jem wrote:
>
>
> Hi Justin and Jianguo,
>
> Thank you for the suggestions. It makes sense to use the same velocities
> from the equilibration output instead of generating them and also to couple
> the groups separately. However they dont seem to work.
>
> I changed the gen_vel to 0 and used the cpt files and equilibration tpr
> files to generate the tpr files for the replica exchange runs but still got
> the bad contacts error.
>
> t = 2.010 ps: Water molecule starting at atom 21424 can not be settled.
> Check for bad contacts and/or reduce the timestep.
> Wrote pdb files with previous and current coordinates
> Jul  5 23:10:10 2011 32736 4 7.04 handleTSRegisterTerm(): TS reports task
> <5> pid <10337> on host killed or core dumped
>
>
> I generated the tpr files with the following command:
>
> /ifs1/apps/gromacs-405/bin/grompp -f remd.mdp -c eq_1ns.tpr -o cptremd0.tpr
> -t eq_1ns.cpt -p popc_mlt.top
>
>
> I then coupled the components of the system separately and even that gave
> the same error.
>
>
> t = 2.018 ps: Water molecule starting at atom 7015 can not be settled.
> Check for bad contacts and/or reduce the timestep.
> Wrote pdb files with previous and current coordinates
> Jul  6 00:13:11 2011 7377 4 7.04 handleTSRegisterTerm(): TS reports task
> <1> pid <24584> on host killed or core dumped
>
> I attach the mdp file that I used. I would appreciate any other suggestions
> you might have.
>
>
> The usual advice is here
> http://www.gromacs.org/Documentation/Terminology/Blowing_Up.
>
> Give up on REMD until you get basic equilibration working.
>
> Mark
>
>
> Thanks
>
> Sheeba
>
>
>
>
>
>
>
>
>
> On Tue, Jul 5, 2011 at 7:22 PM, Justin A. Lemkul  wrote:
>
>>
>>
>> Sheeba Jem wrote:
>>
>>>
>>> Dear Gromacs users,
>>>
>>>  I am having trouble running REMD for a system containing one peptide
>>> molecule on the surface of a lipid membrane, the system contains the
>>> following:
>>>
>>> Protein   1
>>> POPC128
>>> Water 4847
>>> Na+ 9
>>> Cl-  15
>>>
>>> The total number of atoms in the system is 21483. I have 50 replicas with
>>> temperatures distributed from 250 to 400 K. After setting up the system I
>>> minimized and  equilibrated the system for 14 ns at three temperatures: 250
>>> K, 300K and 350 K. I take the output file from the 250 K run and use that as
>>> the starting structure for the temperatures between 250 to 300 K; similarly
>>> the output file from 300 K as the starting structure for replicas between
>>> 300 to 350 K and for the replicas between 350 to 400 K I use the output from
>>> the 350 K run. I further equilibrate these structures at the replica
>>> temperature for 10 ns. The output from these 10 ns runs are then used as
>>> starting structures for the replica exchange simulation. However when the
>>> replica exchange simulation begins to run, it crashes after 2 ps with a bad
>>> contact error:
>>>
>>>
>>  Your equilibration protocol doesn't make much sense.  First, you're not
>> equilibrating properly under all conditions, and then (in your .mdp file)
>> you're re-generating velocities so you just end up destroying any
>> equilibration you had previously achieved.  Membranes are particularly
>> sensitive to proper equilibration, so I suspect this is your root problem.
>>  Equilibrate each system at the desired temperature, maintaining the
>> ensemble by passing the appropriate .cpt file to grompp (with "gen_vel = no"
>> so as not to override the existing velocities).
>>
>>
>>
>>> t = 2.008 ps: Water molecule starting at atom 21421 can not be settled.
>>> Check for bad contacts and/or reduce the timestep.
>>> Wrote pdb files with previous and current coordinates
>>> Jul  4 18:07:21 2011 22666 4 7.04 handleTSRegisterTerm(): TS reports task
>>> <7> pid <15856> on 

[gmx-users] XTC I/O error in replica exchange

[Sanku M]

Hi,
  I am running a replica exchange simulation using 64 replicas ( using 
gromacs4.0.7) in a super computer using 2 nodes ( each having 32 processors). 
But, what happens is that after running for a day or so, the simulation crashes 
with error like 'XTC error, may be you are out of quota'. But, I have checked 
the disc space with the sysadmin and there is no lack of disc space. I am not 
sure what is causing this problem. Any help will be appreciated. 
Sanku-- 
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Re: [gmx-users] Force components on ATOM XX

[Mark Abraham]

On 14/07/2011 9:31 PM, nahren manuel wrote:

Dear Gromacs Users,
Is it possible to get the forces (components, x,y, z) acting on each 
atom from the simulation  or from the rerun.


Sure. Check out nstfout in chapter 7 of the manual, and g_traj -h.

Mark


I need them to calculate the Hessian
Similar to
http://www.sciencedirect.com/science/article/pii/S0006349507715989

Best,
nahren


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Re: [gmx-users] REMD with 'bad contacts' error

[Mark Abraham]

On 15/07/2011 12:40 AM, Sheeba Jem wrote:


Hi, I had been trying different thermostats, barostats, time steps and 
coupling times to get remd for the peptide lipid system working and I 
had even equilibrated each replica for 50 ns before submitting them to 
remd. However none of them work when I use one processor per replica. 
That is, I have 50 replicas and when I submit the job with 50 
processors the job crashes with the bad contacts error.


How soon? Under what REMD regime? The volume scaling required for NPT 
REMD can occasionally be problematic.


However when I use 4 processors per replica that is 200 processors 
instead of 50 then the job runs fine without any problem.


Probably that's just getting lucky with a starting configuration that's 
still got some kind of problem. Without seeing .mdp files, descriptions 
of simulation contents, preparation protocols and actual series of 
command lines, we can't tell what. If you can take the same .tpr files 
that sometimes cause problems with REMD, and successfully use them in 
non-REMD simulations on a range of differently-sized processor sets, 
then you might have evidence of a problem - but the REMD code is stable 
and well tested by now.


Mark

So I went back to the equilibrated systems described in my first mail 
and used the nose hoover thermostat, parinello-rahman semi-isotropic 
pressure coupling, coupled the protein, lipid, water and ions 
separately with no velocity generation and used 4 processors per 
replica and the simulation runs fine. I had ran a 20 ns remd run and 
it has completed successfully but for the exact same tpr files when I 
use 1 processor per replica I get the bad contacts error. Could the 
remd crashing have been due to some scaling issue? if so, the error in 
the log files with 'bad contacts' was misleading...


Sheeba





On Wed, Jul 6, 2011 at 1:06 AM, Mark Abraham > wrote:


On 6/07/2011 2:49 PM, Sheeba Jem wrote:


Hi Justin and Jianguo,

Thank you for the suggestions. It makes sense to use the same
velocities from the equilibration output instead of generating
them and also to couple the groups separately. However they dont
seem to work.

I changed the gen_vel to 0 and used the cpt files and
equilibration tpr files to generate the tpr files for the replica
exchange runs but still got the bad contacts error.

t = 2.010 ps: Water molecule starting at atom 21424 can not be
settled.
Check for bad contacts and/or reduce the timestep.
Wrote pdb files with previous and current coordinates
Jul  5 23:10:10 2011 32736 4 7.04 handleTSRegisterTerm(): TS
reports task <5> pid <10337> on host killed or core dumped


I generated the tpr files with the following command:

/ifs1/apps/gromacs-405/bin/grompp -f remd.mdp -c eq_1ns.tpr -o
cptremd0.tpr -t eq_1ns.cpt -p popc_mlt.top


I then coupled the components of the system separately and even
that gave the same error.


t = 2.018 ps: Water molecule starting at atom 7015 can not be
settled.
Check for bad contacts and/or reduce the timestep.
Wrote pdb files with previous and current coordinates
Jul  6 00:13:11 2011 7377 4 7.04 handleTSRegisterTerm(): TS
reports task <1> pid <24584> on host killed or core dumped

I attach the mdp file that I used. I would appreciate any other
suggestions you might have.


The usual advice is here
http://www.gromacs.org/Documentation/Terminology/Blowing_Up.

Give up on REMD until you get basic equilibration working.

Mark



Thanks

Sheeba









On Tue, Jul 5, 2011 at 7:22 PM, Justin A. Lemkul mailto:jalem...@vt.edu>> wrote:



Sheeba Jem wrote:


Dear Gromacs users,

 I am having trouble running REMD for a system containing
one peptide molecule on the surface of a lipid membrane,
the system contains the following:

Protein   1
POPC128
Water 4847
Na+ 9
Cl-  15

The total number of atoms in the system is 21483. I have
50 replicas with temperatures distributed from 250 to 400
K. After setting up the system I minimized and
 equilibrated the system for 14 ns at three temperatures:
250 K, 300K and 350 K. I take the output file from the
250 K run and use that as the starting structure for the
temperatures between 250 to 300 K; similarly the output
file from 300 K as the starting structure for replicas
between 300 to 350 K and for the replicas between 350 to
400 K I use the output from the 350 K run. I further
equilibrate these structures at the replica temperature
for 10 ns. The output from these 10 ns runs are then used
as starting structures for the replica exchange
simulation. Howeve

Re: [gmx-users] XTC I/O error in replica exchange

[Mark Abraham]

On 15/07/2011 3:06 AM, Sanku M wrote:

Hi,
  I am running a replica exchange simulation using 64 replicas ( using 
gromacs4.0.7) in a super computer using 2 nodes ( each having 32 
processors). But, what happens is that after running for a day or so, 
the simulation crashes with error like 'XTC error, may be you are out 
of quota'. But, I have checked the disc space with the sysadmin and 
there is no lack of disc space. I am not sure what is causing this 
problem. Any help will be appreciated.

Sanku


All kinds of file system hiccups can cause this, including a file 
growing too large for some kinds of file systems, or an NFS server not 
making a file available. It should be possible to observe the same 
phenomenon when not using REMD.


Mark
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Re: [gmx-users] XTC I/O error in replica exchange

[Matthew Zwier]

Hi Sanku,

How large is your XTC file?  This error also shows up when the XTC
file grows too large for the filesystem it's on (frequently 16 GB for
ext3 filesystems on Linux, for example).

MZ

On Thu, Jul 14, 2011 at 1:06 PM, Sanku M  wrote:
> Hi,
>   I am running a replica exchange simulation using 64 replicas ( using
> gromacs4.0.7) in a super computer using 2 nodes ( each having 32
> processors). But, what happens is that after running for a day or so, the
> simulation crashes with error like 'XTC error, may be you are out of quota'.
> But, I have checked the disc space with the sysadmin and there is no lack of
> disc space. I am not sure what is causing this problem. Any help will be
> appreciated.
> Sanku
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[gmx-users] Weird problem

[Sayan Bagchi]

Hello All,
I am having a weird problem and I do not know whether it has to do anything
with Gromacs or the cluster setting I am using.
When I run a MD simulation (on any protein), the job automatically
terminates overnight without an error message. I mean if I start the job
early in the morning it runs longer than if I start the job later in the
day. But it never runs to the desired length mentioned in the .mdp file.

I am copying the .mdp file:

-

integrator  = md
nsteps  = 500
dt  = 0.002
nstlist = 10
nstcomm = 1
rlist   = 1.0
coulombtype = pme
rcoulomb= 1.0
vdw-type= cut-off
rvdw= 1.0
tcoupl  = Nose-Hoover
tc-grps = protein non-protein
tau-t   = 0.5 0.5
ref-t   = 298 298
Pcoupl  =  Parrinello-Rahman
pcoupltype  =  isotropic
tau_p   =  1.0
compressibility =  4.5e-5
ref_p   =  1.0
nstxout = 100
nstvout = 100
nstxtcout   = 100
nstenergy   = 100
userint1= 123
userint2= 124
userint3= 247
---

Any thoughts?

Sayan.
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Re: [gmx-users] Weird problem

[Justin A. Lemkul]

Sayan Bagchi wrote:

Hello All,
I am having a weird problem and I do not know whether it has to do 
anything with Gromacs or the cluster setting I am using.
When I run a MD simulation (on any protein), the job automatically 
terminates overnight without an error message. I mean if I start the job 
early in the morning it runs longer than if I start the job later in the 
day. But it never runs to the desired length mentioned in the .mdp file.




If you are not receiving any error messages from Gromacs, then it is something 
your system is doing that is unrelated to mdrun.  Contact your system 
administrators.  Some queues employ systems to purge jobs after a certain amount 
of time or even stop all jobs at a certain time of day to allow other jobs to start.


-Justin


I am copying the .mdp file:

-

integrator  = md
nsteps  = 500
dt  = 0.002
nstlist = 10
nstcomm = 1
rlist   = 1.0
coulombtype = pme
rcoulomb= 1.0
vdw-type= cut-off
rvdw= 1.0
tcoupl  = Nose-Hoover
tc-grps = protein non-protein
tau-t   = 0.5 0.5
ref-t   = 298 298
Pcoupl  =  Parrinello-Rahman
pcoupltype  =  isotropic
tau_p   =  1.0
compressibility =  4.5e-5
ref_p   =  1.0
nstxout = 100
nstvout = 100
nstxtcout   = 100
nstenergy   = 100
userint1= 123
userint2= 124
userint3= 247
---

Any thoughts?

Sayan.





--


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] Replicate Triclinic Bilayer

[Max Watson]

I would like to replicate the tilted DPPC gel phase from Marrink's website
laterally, so that I have 4 times the area. But since the coupling is
anisotropic, there are 9 box dimensions, and the triclinic geometry confuses
me.

I have seen that you can use editconf and -translate, followed by merging
the .gro files when using orthogonal box lengths Lx, Ly Lz. But what are the
new dimensions of my replicated triclinic system?

Also, if anyone can tell me about a good website or book that describes
triclinic geometry using lots of pictures, I'd really appreciate it.

Thanks!

Max
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Re: [gmx-users] Replicate Triclinic Bilayer

[Justin A. Lemkul]

Max Watson wrote:
I would like to replicate the tilted DPPC gel phase from Marrink's 
website laterally, so that I have 4 times the area. But since the 
coupling is anisotropic, there are 9 box dimensions, and the triclinic 
geometry confuses me.


I have seen that you can use editconf and -translate, followed by 
merging the .gro files when using orthogonal box lengths Lx, Ly Lz. But 
what are the new dimensions of my replicated triclinic system?




Use genconf -nbox to replicate the system in any way you like.

Also, if anyone can tell me about a good website or book that describes 
triclinic geometry using lots of pictures, I'd really appreciate it.




A few minutes on Google turns up tons of images.  There's also a bit in 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] g_dist with multiple chains of molecules

[Sanku M]

Hi,
  I am running a simulation where I have 100 chains of molecule in a box . I am 
trying to calculate the distance between two particular atoms ( present in each 
molecule)  averaged over all the chains of molecule. i.e If I have atom C1 and 
C2 in each of the molecule-chain, I want to calculate the distance between C1 
and C2 atom in each chain and average over them.
I was trying to use gromacs 4.0.7  g_dist tool . For that, I first created two 
 index-groups  of all C1 and C2 . But. I realized that g_dist will give me 
actually the distance between center of mass of all C1 and center of mass of 
all 
C2 which is NOT certainly I was looking for.
 So, I was wondering whether there is any other tool which can split the entire 
index group by deviding it by total number of chains and then calculate each 
individual distances for each chain and then do an average over them.


An analogous tool exists for g_gyrate where where one can use -nmol option to 
split the entire index accordingly and calculate the radius of gyration 
averaged 
over all the molecules. I was looking for something for calculating distances 
between two atoms for many chain molecules.

I looked at the mailing list but I could not find any solutions for these. Any 
help will be appreciated.

Sanku-- 
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Re: [gmx-users] g_dist with multiple chains of molecules

[Justin A. Lemkul]

Sanku M wrote:

Hi,
  I am running a simulation where I have 100 chains of molecule in a box 
. I am trying to calculate the distance between two particular atoms ( 
present in each molecule)  averaged over all the chains of molecule. i.e 
If I have atom C1 and C2 in each of the molecule-chain, I want to 
calculate the distance between C1 and C2 atom in each chain and average 
over them.
I was trying to use gromacs 4.0.7  g_dist tool . For that, I first 
created two  index-groups  of all C1 and C2 . But. I realized that 
g_dist will give me actually the distance between center of mass of all 
C1 and center of mass of all C2 which is NOT certainly I was looking for.
 So, I was wondering whether there is any other tool which can split the 
entire index group by deviding it by total number of chains and then 
calculate each individual distances for each chain and then do an 
average over them.




You can split the group within make_ndx.  There are various splitting keywords 
(like 'splitat' or 'splitres') that can divide up your index groups.  Then 
script the 100 calls to g_dist.


-Justin



An analogous tool exists for g_gyrate where where one can use -nmol 
option to split the entire index accordingly and calculate the radius of 
gyration averaged over all the molecules. I was looking for something 
for calculating distances between two atoms for many chain molecules.


I looked at the mailing list but I could not find any solutions for 
these. Any help will be appreciated.


Sanku
 



--


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] malloc on mac

[Itamar Kass]

Hi all,

I am trying to find all possible h-bonds between chains in my complex. I 
am using:


g_hbond_d -f system_run1_MD050_fitbb.xtc -s system_for_EM.tpr -n 
system.ndx -g system_run1_MD050_fitbb_Hbond_all.log -num 
system_run1_MD050_fitbb_Hbnum_all.xvg -hbn 
system_run1_MD050_fitbb.xtc_Hbond_all.ndx


and after reading 100ns the system crash and report:

Reading frame1000 time 10.000   g_hbond_d(42677) malloc: *** 
error for object 0xd: pointer being reallocated was not allocated

*** set a breakpoint in malloc_error_break to debug

I am suing gromacs 4.0.7 (double precision) on mac (10.6.8), which I 
compiled myself (not via fink). I also tried to compile it using dmalloc 
without success.


Thanks in advance for any idea,
Itamar

--


"In theory, there is no difference between theory and practice. But, in practice, 
there is." - Jan L.A. van de Snepscheut

===
| Itamar Kass, Ph.D.
| Postdoctoral Research Fellow
|
| Department of Biochemistry and Molecular Biology
| Building 77 Clayton Campus
| Wellington Road
| Monash University,
| Victoria 3800
| Australia
|
| Tel: +61 3 9902 9376
| Fax: +61 3 9902 9500
| E-mail: itamar.k...@monash.edu


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Re: [gmx-users] g_dist with multiple chains of molecules

[Mark Abraham]

On 15/07/2011 6:37 AM, Sanku M wrote:

Hi,
  I am running a simulation where I have 100 chains of molecule in a 
box . I am trying to calculate the distance between two particular 
atoms ( present in each molecule)  averaged over all the chains of 
molecule. i.e If I have atom C1 and C2 in each of the molecule-chain, 
I want to calculate the distance between C1 and C2 atom in each chain 
and average over them.
I was trying to use gromacs 4.0.7  g_dist tool . For that, I first 
created two  index-groups  of all C1 and C2 . But. I realized that 
g_dist will give me actually the distance between center of mass of 
all C1 and center of mass of all C2 which is NOT certainly I was 
looking for.
 So, I was wondering whether there is any other tool which can split 
the entire index group by deviding it by total number of chains and 
then calculate each individual distances for each chain and then do an 
average over them.


Check out g_dist -h. There are some other tools suggested there that 
look at inter-group distances in a different ways, and one of them works 
well for you.


Mark

An analogous tool exists for g_gyrate where where one can use -nmol 
option to split the entire index accordingly and calculate the radius 
of gyration averaged over all the molecules. I was looking for 
something for calculating distances between two atoms for many chain 
molecules.


I looked at the mailing list but I could not find any solutions for 
these. Any help will be appreciated.


Sanku


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Re: [gmx-users] malloc on mac

[Mark Abraham]

On 15/07/2011 11:48 AM, Itamar Kass wrote:

Hi all,

I am trying to find all possible h-bonds between chains in my complex. 
I am using:


g_hbond_d -f system_run1_MD050_fitbb.xtc -s system_for_EM.tpr -n 
system.ndx -g system_run1_MD050_fitbb_Hbond_all.log -num 
system_run1_MD050_fitbb_Hbnum_all.xvg -hbn 
system_run1_MD050_fitbb.xtc_Hbond_all.ndx


and after reading 100ns the system crash and report:

Reading frame1000 time 10.000   g_hbond_d(42677) malloc: *** 
error for object 0xd: pointer being reallocated was not allocated

*** set a breakpoint in malloc_error_break to debug

I am suing gromacs 4.0.7 (double precision) on mac (10.6.8), which I 
compiled myself (not via fink). I also tried to compile it using 
dmalloc without success.


Sounds like a bug. Try g_hbond from a more recent version of GROMACS.

BTW, you should only compile and use tools in double precision if that 
extra accuracy is what you actually need. Otherwise you're just running 
slower than you need to. All tools can read files written at either 
precision.


Mark
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[gmx-users] monte carlo simulation in gromacs

[sreelakshmi ramesh]

Dear all,
I wanted to do perform a Monte carlo simulation of  RNA
using coarse grained force filedn in gromacs.when i do pdb2gmx i dont get
option for Coarse grained ff.is mC integrator availble in gromacs?

thanks in advance,
sree.
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Re: [gmx-users] monte carlo simulation in gromacs

[Mark Abraham]

On 15/07/2011 1:25 PM, sreelakshmi ramesh wrote:

Dear all,
I wanted to do perform a Monte carlo simulation of  
RNA using coarse grained force filedn in gromacs.when i do pdb2gmx i 
dont get option for Coarse grained ff.is  mC integrator 
availble in gromacs?


GROMACS doesn't do MC at all. Coarse-grained force fields can be added, 
but are not in the main distribution.


Mark
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