[gmx-users] Simulation Crash...Reg

[Kishore]

Dear All,
I am simulating a tetramer (Alcohol Dehydrogenase with bound NADPH) in
simple spc water in a dodecahedron box. I could easily walk through till the
NVT equilibration step after which every thing seems so right(after 5
steps with time step of 2fs using V-rescale thermostat the system
equilibrates to T=300K). But the NPT equilibration ( for 5 steps with
time step of 2fs using Parrinello-rahman barostat) is crashing( after 1
steps) with too many LINCS warnings. Looking at the log file I understand
there are very high fluctuations in the temperatures after a few steps from
the start of the simulation. What can be the possible reason for this kind
of a behavior and what can be done to fix it?

-- 
KRISHNA KISHORE@IIT-MADRAS
-- 
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] Input files for g_bar

[Justin A. Lemkul]

Warren Gallin wrote:

Hi,

I am working my way through learning to use g_bar to obtain a PMF curve.

As far as I can see, the input for g_bar can be hundreds of files.  Is 
there some general way to feed a large number of file names to a program other 
than typing them individually on the command line?



g_bar -f *.xvg

-Justin

Warren Gallin-- 
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



--


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


--
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] Input files for g_bar

[Warren Gallin]

Hi,

I am working my way through learning to use g_bar to obtain a PMF curve.

As far as I can see, the input for g_bar can be hundreds of files.  Is 
there some general way to feed a large number of file names to a program other 
than typing them individually on the command line?

Warren Gallin--
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] Re: distance restraints for atoms on 2 chains

[Justin A. Lemkul]

Sai Pooja wrote:

Hi
 
This is regarding the pull code.. I have followed your tutorial to get 
the PMF for distance between 2 atoms using the pull code. I want to know 
if one can bring the atoms closer rather than pull them apart? I want to 


Set pull_rate < 0.

start from the maximum distance and then bring them closer to check 
reversibility. Also, I dont think I can apply it a fixed vector (as in 
specify the vector from one atom to the other) because I dont think the 
path will be a straight line.
 


All pulling is conducted along a vector, either by specifying pull_vec or 
pull_dim.

-Justin


Pooja

On Fri, Apr 1, 2011 at 8:02 PM, Justin A. Lemkul > wrote:




Sai Pooja wrote:

The pull tutorial uses npt simulations.. is that required by the
algorithm or can one use nvt after the system has been
sufficiently equilibrated using npt?


Use whatever conditions are appropriate for your system.  Tutorials
should not be viewed as the only applicable conditions, merely one
such example of what might be done.

-Justin

On Fri, Apr 1, 2011 at 7:32 PM, Justin A. Lemkul
mailto:jalem...@vt.edu>
>> wrote:


   pdb2gmx -chainsep (-merge in 4.0.x and before) should allow
you to
   create a merged [moleculetype] to apply distance restraints.  If
   you're just trying to use a harmonic potential to define some
   sampling distance (for US), then distance restraints are not
   necessary, just apply the pull code.

   -Justin

   Sai Pooja wrote:

   Also, the chains do not diffuse apart in time since they are
   position restrained(some parts of each chain are ...)

   On Fri, Apr 1, 2011 at 7:26 PM, Sai Pooja
mailto:saipo...@gmail.com>
   >


     | (540)
231-9080 
   

   http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

   
   -- 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




-- 
Quaerendo Invenietis-Seek and you shall discover.



-- 



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


-- 
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




--
Quaerendo Invenietis-Seek and you shall discover.


--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Tr

Re: [gmx-users] Heat of vap

[Justin A. Lemkul]

Elisabeth wrote:

Dear David,

I followed your instructions and calculated Heat of vaporization of my 
alkane once with one molecule in gas phase (no cutoff) and once with 
equivalent number of molecules as in liquid phase as Justin suggested. 
Results are as follows:




To get heat of vaporization, you shouldn't be simulating just a single molecule 
in the gas phase, it should be an equivalent number of molecules as you have in 
the liquid phase.



*one single molecule in gas phase*

Energy  Average   Err.Est.   RMSD  Tot-Drift
---
LJ (SR)-2.24473  0.073  1.292   0.342696  
(kJ/mol)
Coulomb (SR)11.5723   0.552.17577   -2.33224  
(kJ/mol)
Potential  *  59.244 *  0.9410.97566.35631  
(kJ/mol)
Total Energy106.647  115.48286.78792  
(kJ/mol)


*equivalent number of molecules as in liquid* ( large box 20 nm)

Statistics over 101 steps [ 0. through 2000. ps ], 4 data sets
All statistics are over 11 points

Energy  Average   Err.Est.   RMSD  Tot-Drift
---
LJ (SR)-2.16367  0.053   0.171542   0.374027  
(kJ/mol)
Coulomb (SR)11.2894   0.230.49105   -1.44437  
(kJ/mol)
Potential *  63.2369*1.12.472117.69756  
(kJ/mol)
Total Energy114.3371.12.655477.72258  
(kJ/mol)



 Since pbc is set to NO molecules leave the box and I dont know if this 
all right. I hope the difference is acceptable...!




For "pbc = no" there is no box.

0- I am going to do the same calculation but for some polymers solvated 
in the alkane. For binary system do I need to look at nonboded terms? 
and then run a simulation for a single polymer in vacuum?


Can you please provide me with a recipe for Delta Hvap of the solute in 
a solvent?




The method for calculating heat of vaporization is not dependent upon the 
contents of the system; it is a fundamental thermodynamic definition.  Heat of 
vaporization is not something that can be calculated from a solute in a solvent. 
 You can calculate DHvap for a particular system, but not some subset of that 
system.




1- If I want to look at nonboded interactions only, do I have to add  
Coul. recip.  to [ LJ (SR)  + Coulomb (SR) ] ?





The PME-related terms contain both solute-solvent, solvent-solvent, and 
potentially solute-solute terms (depending on the size and nature of the 
solute), so trying to interpret this term in some pairwise fashion is an 
exercise in futility.


-Justin

coulombtype =  PME  
vdw-type=  Shift   
rcoulomb-switch =  0  
rvdw-switch =  0.9
rlist   =  1.2   
rcoulomb=  1.2
rvdw=  1.0   



ff: OPLSAA


Appreciate your help,
Best,



--


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


--
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 with new format of angletypes

[Justin A. Lemkul]

Hyunjin Kim wrote:

Dear,

When I generated bond parameters as following and ran "grompp", then I had
an error messages "No default Angle types"


[ angletypes ]
; i j   k   functh0 cth ub0 cub
OST CST OST 5   180.25104.0 0.0 0.0
CS  SS  FE  5   100.6   418.4   0.0 0.0
..


When "func" number was chosen to "1" and removed "ub0" and "cub" terms,
the error did not occurred. Does anyone know how to use the above angle
types in the parameter file without any error, please let me know. I


The error comes from the fact that you're defining an angletype that does not 
exist.  You shouldn't be hacking ffbonded.itp to try to solve this problem, you 
should be making sure that your topology calls angletypes that are actually 
present in the force field.  If they're not, either define them manually or use 
a different force field that is suited to your application.  Hacking the 
ffbonded.itp file is a great way to invalidate a force field.



appreciate that in advance. Can this problem be related to the version of
gromacs? I am sure that gromacs I have here is 4.0. or higher, but it
might not be 4.5. or higher.



Based on the fact that this snippet appears to be from the CHARMM force field, 
you're probably using 4.5 or higher.  If you don't know, you can find out by 
issuing any command with the -h argument and reading the information printed, 
among which the "VERSION" string should be prominent.  After you know what 
you're using, refer to the appropriate manual and any information therein about 
how to properly use the force field you want.


-Justin


Thanks.

Hyunjin.





--


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


--
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] Re: distance restraints for atoms on 2 chains

[Sai Pooja]

Hi

This is regarding the pull code.. I have followed your tutorial to get the
PMF for distance between 2 atoms using the pull code. I want to know if one
can bring the atoms closer rather than pull them apart? I want to start from
the maximum distance and then bring them closer to check reversibility.
Also, I dont think I can apply it a fixed vector (as in specify the vector
from one atom to the other) because I dont think the path will be a straight
line.

Pooja

On Fri, Apr 1, 2011 at 8:02 PM, Justin A. Lemkul  wrote:

>
>
> Sai Pooja wrote:
>
>> The pull tutorial uses npt simulations.. is that required by the algorithm
>> or can one use nvt after the system has been sufficiently equilibrated using
>> npt?
>>
>>
> Use whatever conditions are appropriate for your system.  Tutorials should
> not be viewed as the only applicable conditions, merely one such example of
> what might be done.
>
> -Justin
>
>  On Fri, Apr 1, 2011 at 7:32 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>pdb2gmx -chainsep (-merge in 4.0.x and before) should allow you to
>>create a merged [moleculetype] to apply distance restraints.  If
>>you're just trying to use a harmonic potential to define some
>>sampling distance (for US), then distance restraints are not
>>necessary, just apply the pull code.
>>
>>-Justin
>>
>>Sai Pooja wrote:
>>
>>Also, the chains do not diffuse apart in time since they are
>>position restrained(some parts of each chain are ...)
>>
>>On Fri, Apr 1, 2011 at 7:26 PM, Sai Pooja > >
>>>> wrote:
>>
>>   Hi,
>>I have 5 chains in my Protein. I want to apply distance
>>restraints
>>   for doing Umbrella Sampling for 2 atoms on different chains. Is
>>   there a way to do this since the two chains have separater
>>itp files.
>>Pooja
>>
>>   -- Quaerendo Invenietis-Seek and you shall discover.
>>
>>
>>
>>
>>-- Quaerendo Invenietis-Seek and you shall discover.
>>
>>
>>-- 
>>
>>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
>>
>>
>>-- 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
>>
>>
>>
>>
>> --
>> Quaerendo Invenietis-Seek and you shall discover.
>>
>
> --
> 
>
> 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
>
> 
> --
> 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
>



-- 
Quaerendo Invenietis-Seek and you shall discover.
-- 
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] grompp error with new format of angletypes

[Hyunjin Kim]

Dear,

When I generated bond parameters as following and ran "grompp", then I had
an error messages "No default Angle types"


[ angletypes ]
; i j   k   functh0 cth ub0 cub
OST CST OST 5   180.25104.0 0.0 0.0
CS  SS  FE  5   100.6   418.4   0.0 0.0
..


When "func" number was chosen to "1" and removed "ub0" and "cub" terms,
the error did not occurred. Does anyone know how to use the above angle
types in the parameter file without any error, please let me know. I
appreciate that in advance. Can this problem be related to the version of
gromacs? I am sure that gromacs I have here is 4.0. or higher, but it
might not be 4.5. or higher.

Thanks.

Hyunjin.



-- 
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] Heat of vap

[Elisabeth]

Dear David,

I followed your instructions and calculated Heat of vaporization of my
alkane once with one molecule in gas phase (no cutoff) and once with
equivalent number of molecules as in liquid phase as Justin suggested.
Results are as follows:

*one single molecule in gas phase*

Energy  Average   Err.Est.   RMSD  Tot-Drift
---
LJ (SR)-2.24473  0.073  1.292   0.342696
(kJ/mol)
Coulomb (SR)11.5723   0.552.17577   -2.33224
(kJ/mol)
Potential  *  59.244 *  0.9410.97566.35631
(kJ/mol)
Total Energy106.647  115.48286.78792
(kJ/mol)

*equivalent number of molecules as in liquid* ( large box 20 nm)

Statistics over 101 steps [ 0. through 2000. ps ], 4 data sets
All statistics are over 11 points

Energy  Average   Err.Est.   RMSD  Tot-Drift
---
LJ (SR)-2.16367  0.053   0.171542   0.374027
(kJ/mol)
Coulomb (SR)11.2894   0.230.49105   -1.44437
(kJ/mol)
Potential *  63.2369*1.12.472117.69756
(kJ/mol)
Total Energy114.3371.12.655477.72258
(kJ/mol)


 Since pbc is set to NO molecules leave the box and I dont know if this all
right. I hope the difference is acceptable...!

0- I am going to do the same calculation but for some polymers solvated in
the alkane. For binary system do I need to look at nonboded terms? and then
run a simulation for a single polymer in vacuum?

Can you please provide me with a recipe for Delta Hvap of the solute in a
solvent?


1- If I want to look at nonboded interactions only, do I have to add  Coul.
recip.  to [ LJ (SR)  + Coulomb (SR) ] ?


coulombtype =  PME
vdw-type=  Shift
rcoulomb-switch =  0
rvdw-switch =  0.9
rlist   =  1.2
rcoulomb=  1.2
rvdw=  1.0


ff: OPLSAA


Appreciate your help,
Best,
-- 
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] smooth trajectory

[Justin A. Lemkul]

ana johari wrote:

dear Justin,

tanks for your kindness.I would like to follow up what you say,but I 
want to have simulation without wraping.

could these command be helpful?


No.  A modified trajectory should not be used for further simulation.  "Fixing" 
periodicity is only useful for visualization and, in some cases, proper 
analysis.  All simulations should be conducted from unmodified files.


-Justin

trjconv -s first1ns.tpr -f whatever_trajectory_you_want(xtc after 3ns 
simulation).xtc -pbc mol -center -o fit.gro

 grompp -f md300.mdp -c fit.gro -p n.top -o md300.tpr -n n.ndx
 nohup mpirun -np 8 mdrun -s md300.tpr  -o md300.trr -c md300.gro -g 
md300.log -e md300.edr&

best regards

ana johari wrote:
 > dear user,
 >
 > Tanks for your advice,
 >
 > But the mdrun is know on the step of 33562880  but the protein was 
split at the first 1ns of MD. is  it necessary to use 
“tpbconv” command and extract the *.tpr file just after first 1 ns and  
then use trjconv –ur compact as command.

 >

No.  If the starting configuration had the protein properly centered in 
the box, then a simple:


trjconv -s first.tpr -f whatever_trajectory_you_want.xtc -pbc mol -center

should work to make molecules whole and center the protein in the box.

-Justin

 > Best regards,
 >
 >
 > 
 > *From:* Justin A. Lemkul mailto:jalem...@vt.edu>>
 > *To:* Discussion list for GROMACS users >

 > *Sent:* Fri, April 1, 2011 2:52:53 PM
 > *Subject:* Re: [gmx-users] FW: protein split over boundary
 >
 >
 >
 > ana johari wrote:
 >  > Dear user,
 >  >
 >  > Tanks for your attention ,I read about trjconv,but I want to know 
is it necessary  to back to the exact fram befor molecule split happens 
and then center the molecule by trjconv command?

 >  >
 >
 > If the protein starts in the center of the box, just use trjconv in 
conjunction with your original .tpr file.  A suggested trjconv workflow 
is on the page Tsjerk pointed you to.

 >
 >  > The other point,if you attention to my value”edit conf  d=0.9 and 
during MD rvdw=1..4” is it broke the rule of periodic boundary condition 
or not?

 >  >
 >
 > In principle, no, as long as your box does not significantly deform.  
Check with g_mindist -pi.

 >
 > -Justin
 >
 >  > tanks
 >  >
 >  >
 >  >
 >  > 

 >  > *From:* Tsjerk Wassenaar  >>
 >  > *To:* Discussion list for GROMACS users  >>

 >  > *Sent:* Fri, April 1, 2011 1:29:19 PM
 >  > *Subject:* Re: [gmx-users] FW: protein split over boundary
 >  >
 >  > 
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

 >  >
 >  > -TAW
 >  >
 >  > On Fri, Apr 1, 2011 at 10:53 AM, anahita  >    >  >
 >  >  >
 >  >  >
 >  >  >
 >  >  > From: anahita [mailto:ana_j0...@yahoo.com 
 >  >>]

 >  >  > Sent: Friday, April 01, 2011 1:13 PM
 >  >  > To: 'gmx-users-requ...@gromacs.org 
 
> 
 
>>'

 >  >  > Subject: protein split over boundary
 >  >  >
 >  >  >
 >  >  >
 >  >  > Dear user,
 >  >  >
 >  >  > Hello, I appreciate if somebody help me. During the simulation 
of my protein

 >  >  > I didn’t get any error but after 1ns of MD
 >  >  >
 >  >  > my molecule was split over boundary in cubic box. it means some 
part of it

 >  >  > enter the other side of the box.
 >  >  >
 >  >  > At first,For decreasing the cost of simulation, in “editconf” 
command I set
 >  >  > the number “d” on 0.9  to decease the box size. I want to 
mention that

 >  >  > during the calculation my rvdw is 1.4.
 >  >  >
 >  >  > I want to know instead of problem of visualization, the other 
things is

 >  >  > fine?
 >  >  >
 >  >  > Best regards.
 >  >  >
 >  >  > A. johari
 >  >  >
 >  >  > --
 >  >  > gmx-users mailing listgmx-users@gromacs.org 
 >  >>

 >  >  > http://lists.gromacs.org/mailman/listinfo/gmx-users
 >  

[gmx-users] smooth trajectory

[ana johari]

dear Justin,
tanks for your kindness.I would like to follow up what you say,but I want to 
have simulation without wraping.
could these command be helpful?
trjconv -s first1ns.tpr -f whatever_trajectory_you_want(xtc after 3ns 
simulation).xtc -pbc mol -center -o fit.gro
 grompp -f md300.mdp -c fit.gro -p n.top -o md300.tpr -n n.ndx
 nohup mpirun -np 8 mdrun -s md300.tpr  -o md300.trr -c md300.gro -g md300.log 
-e md300.edr&
best regards


ana johari wrote:
> dear user,
> 
> Tanks for your advice,
> 
> But the mdrun is know on the step of 33562880  but the protein was split at 
> the 
>first 1ns of MD. is  it necessary to use “tpbconv” command and 
>extract the *.tpr file just after first 1 ns and  then use trjconv –ur compact 
>as command.
> 

No.  If the starting configuration had the protein properly centered in the 
box, 
then a simple:

trjconv -s first.tpr -f whatever_trajectory_you_want.xtc -pbc mol -center

should work to make molecules whole and center the protein in the box.

-Justin

> Best regards,
> 
> 
> 
> *From:* Justin A. Lemkul 
> *To:* Discussion list for GROMACS users 
> *Sent:* Fri, April 1, 2011 2:52:53 PM
> *Subject:* Re: [gmx-users] FW: protein split over boundary
> 
> 
> 
> ana johari wrote:
>  > Dear user,
>  >
>  > Tanks for your attention ,I read about trjconv,but I want to know is it 
>necessary  to back to the exact fram befor molecule split happens and then 
>center the molecule by trjconv command?
>  >
> 
> If the protein starts in the center of the box, just use trjconv in 
> conjunction 
>with your original .tpr file.  A suggested trjconv workflow is on the page 
>Tsjerk pointed you to.
> 
>  > The other point,if you attention to my value”edit conf  d=0.9 and during 
>MD 
>rvdw=1..4” is it broke the rule of periodic boundary condition or not?
>  >
> 
> In principle, no, as long as your box does not significantly deform.  Check 
>with g_mindist -pi.
> 
> -Justin
> 
>  > tanks
>  >
>  >
>  >
>  > 
>  > *From:* Tsjerk Wassenaar mailto:tsje...@gmail.com>>
>  > *To:* Discussion list for GROMACS users >
>  > *Sent:* Fri, April 1, 2011 1:29:19 PM
>  > *Subject:* Re: [gmx-users] FW: protein split over boundary
>  >
>  > 
>http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
>  >
>  > -TAW
>  >
>  > On Fri, Apr 1, 2011 at 10:53 AM, anahita  >> wrote:
>  >  >
>  >  >
>  >  >
>  >  >
>  >  > From: anahita [mailto:ana_j0...@yahoo.com  
>>]
>  >  > Sent: Friday, April 01, 2011 1:13 PM
>  >  > To: 'gmx-users-requ...@gromacs.org 
> 
>>'
>  >  > Subject: protein split over boundary
>  >  >
>  >  >
>  >  >
>  >  > Dear user,
>  >  >
>  >  > Hello, I appreciate if somebody help me. During the simulation of my 
>protein
>  >  > I didn’t get any error but after 1ns of MD
>  >  >
>  >  > my molecule was split over boundary in cubic box. it means some part of 
>it
>  >  > enter the other side of the box.
>  >  >
>  >  > At first,For decreasing the cost of simulation, in “editconf” command I 
>set
>  >  > the number “d” on 0.9  to decease the box size. I want to mention that
>  >  > during the calculation my rvdw is 1.4.
>  >  >
>  >  > I want to know instead of problem of visualization, the other things is
>  >  > fine?
>  >  >
>  >  > Best regards.
>  >  >
>  >  > A. johari
>  >  >
>  >  > --
>  >  > 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 list    gmx-users@gromacs.org 
> >
>  > http://lists.gromacs.org/mailman/listinfo/gmx-users
>  > Please search the archive at 
>http://www.gromacs.org/Support/Mailing_L

Re: [gmx-users] g_sasa

[Justin A. Lemkul]

deisy yurley rodriguez sarmiento wrote:

Hey everyone...

I need help I would like to know how to calculate the sasa (solvent 
accesible surface area). What quantum or statiscal method to calculate 
done that?




The tool to use is g_sas.  It prints a citation to the method used in the SASA 
calculation.


-Justin



Deisy Y. Rodriguez S.
Practicante de Computos Avanzados
Grupo de Investigacion en Fisicoquimica Teorica y Experimental GIFTEX
Tel. 6344000  ext. 2792
Universidad Industrial de Santander



--


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


--
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] g_sasa

[deisy yurley rodriguez sarmiento]

Hey everyone...
I need help I would like to know how to calculate the sasa (solvent 
accesible surface area). What quantum or statiscal method to calculate done 
that?

Deisy Y. Rodriguez S.
Practicante de Computos Avanzados
Grupo de Investigacion en Fisicoquimica Teorica y Experimental GIFTEX
Tel. 6344000  ext. 2792
Universidad Industrial de Santander
-- 
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