date:20110120

I want to calculate the rmsd of amino acid 65 to 67 of two simulated
proteins with  loop replacement in another one to find out how the position
of these 3  amino acids change due to the replacement of a loop region in
same protein ... How can I achieve it with gromacs...

-- 
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
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[gmx-users] charge group radii larger that rlist-rvdw

2011-01-20 Thread Kavyashree M

Dear gromacs users,

 I am using gromacs 4.5.3, OPLSAA force field, and the cut off
parameters
are as shown below:
-
;NEIGHBOURSEARCHING PARAMETERS
nstlist = 10 10 ; FREQUENCY WITH WHICH
NEIGHBOURLIST IS UPDATED
ns_type = grid  ; TYPE OF NEIGHBOUR SEARCH
GRID OR SIMPLE
pbc = xyz   ; DIRECTION OF PERIODIC
BOUNDARY CONDITIONS USAGE
rlist   = 1.36  ; CUT-OFF DISTANCE FOR SHORT
RANGE NEIGHBOUR LIST

;ELECTROSTATICS
coulombtype = PME   ; METHOD FOR CALCULATING
COULOMBIC INTERCATION - PME
rcoulomb= 1.36  ; CUTOFF DISTANCE FOR
ELECTROSTATIC INTERACTIONS
epsilon_r   = 1 ; RELATIVE DIELECTRIC
CONSTANT

;VAN DER WAALS
vdwtype = Switch; METHOD FOR TREATING
VANDERWAAL'S FORCES
rvdw_switch = 0.9   ; WHEN TO START SWITCHING LJ
POTENTIAL
rvdw= 1.03  ; CUTOFF DISTANCE FOR LJ OR
BUCKINGHAM INTERACTIONS

;EWALD
fourierspacing  = 0.12  ; GRID SPACING FOR FFT GRID
FOR PME
pme_order   = 4 ; INTERPOLATION ORDER FOR
PME
ewald_rtol  = 1e-5  ; RELATIVE STRENGTH OF EWALD
SHIFTED DIRECT POTENTIAL
optimize_fft= yes   ; SAVES A FEW PERCENT FOR
LONG SIMULATIONS
-

For EM (energy minimisation) I initially had used
rlist = rcolomb = 1.2;  rvdw = 1.1; rvdw_switch = 1.0
grompp gave the message:
##
Largest charge group radii for Van der Waals: 0.160, 0.157 nm
Largest charge group radii for Coulomb:   0.168, 0.167 nm

NOTE 1 [file md.mdp]:
  The sum of the two largest charge group radii (0.317) is larger than
  rlist (1.2) - rvdw (1.1)
##
So I changed the values to: rlist = rcolomb = 1.35;  rvdw = 1.03;
rvdw_switch = 1.0
grompp message during em disappeared.

During PR (position refinement), Again the message appeared for grompp
##
Largest charge group radii for Van der Waals: 0.168, 0.156 nm
Largest charge group radii for Coulomb:   0.168, 0.164 nm

NOTE 1 [file md.mdp]:
  The sum of the two largest charge group radii (0.324) is larger than
  rlist (1.35000) - rvdw (1.03000)
##
hence I  changed the values to: rlist = rcolomb = 1.36;  rvdw = 1.03;
rvdw_switch = 1.0
grompp message during pr disappeared.

The same message repeated for MD
###
Largest charge group radii for Van der Waals: 0.171, 0.159 nm
Largest charge group radii for Coulomb:   0.171, 0.166 nm

NOTE 1 [file md.mdp]:
  The sum of the two largest charge group radii (0.330248) is larger than
  rlist (1.36) - rvdw (1.03)
###

My questions are:
1. Why does the charge group radii change in this way from em to pr to MD
even though I
   am using same parameters
2. What is the safest maximum value of rlist I can go up to? (is it 1.4nm
according to "The Origin
   of Layer Structure Artifacts in Simulations of Liquid Water"- JCTC, 2006,
2, 1-11 paper?)
3. What is the minimum safest rvdw distance i can take?
4. According to the manual, when using switch they have suggested that "..
neighbor search
   cut-off rlist should be 0.1 to 0.3nm larger than rvdw..." then Why in the
above case it goes
   more than 0.3nm?

Thanks in advance
MKS
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Re: [gmx-users] Re: avoiding bad contact in continutation run (Mark Abraham)



> one final query, i need the new tpr to have a different output frequency than 
> the older one, is there a way to achieve that.
> Thanks,
> -Adwait
> 
> 

You have to use the grompp version of restarts for that. See the URL I gave 
earlier.

Mark
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[gmx-users] Re: avoiding bad contact in continutation run (Mark Abraham)




   1. Re: avoiding bad contact in continutation run (MarkAbraham)
Adwait Mevada wrote:



On 01/20/11, Adwait Mevada   wrote:


 Dear gmx-users,
 I am simulating a dppc + chol system, the force field is martini
with gromacs 3.3.3 the system was initially run for 150 ns, but i
had to later extend the simulation, so using the confout.gro and
with mdp options:
gen_vel = no
unconstrained_start = yes
 I gave a re-run for another 850 ns, now due to some interaction  the
box explodes after 460ns of run.I found that the cause was due  to
some unwanted bad contact.
It is important that the system continue from the previous state,
but the extension is leading to this bad contact.



Actually, you didn't preserve your ensemble if you used the .gro  file
for the coordinates. See
http://www.gromacs.org/Documentation/How-tos/Doing_Restarts Actually
 providing us with copies of the commands you're using is always a
good idea when asking for help.


150ns.gro was the output of the previous simulation run i.e. confout.gro
mdp file for the previous simulation is taken as is except for change of
simulation steps and making unconstrained_start = yes
grompp -np 8 -f 850ns.mdp -p dppc_chol.top -c 150ns.gro -o
512lip_256chol_850ns.tpr


As Mark suspected, you have failed to preserve your ensemble, due to
the fact
that you're using a reduced precision (.gro) format for coordinates,
 and you are
not supplying the .trr and .edr file from the previous run, so you're
losing
velocities, temperature and pressure coupling information, etc.

-Justin

so i should be doing something like
tpbconv -s 512lip_150ns.tpr -f 512lip_150ns.trr -e 512lip_150ns.edr -o
512lip_850ns.tpr -extend 850

mpiexe.openmpi -np 8 mdrun_mpi.openmpi -np 8 -s 512lip_850ns.tpr
 -o 512lip_850ns -e 512lip_850ns -g 512lip_850ns &



Yes, that would be an appropriate set of commands to extend the run.

one final query, i need the new tpr to have a different output  
frequency than the older one, is there a way to achieve that.

Thanks,
-Adwait

-Justin


mpiexe.openmpi -np 8 mdrun_mpi.openmpi -np 8 -s 512lip_256chol_850ns.tpr
-o 512lip_256chol_850ns -e 512lip_256chol_850ns -g
512lip_256chol_850ns &


Mark



My question is, is there a way to avoid this while retaining the
continuation of the previous simulation?
 Is using lower precision file a solution to this problem? if yes
how do i go about it.
-Adwait


This message was sent using IMP, the Internet Messaging Program.

--



-Adwait


This message was sent using IMP, the Internet Messaging Program.



--


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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End of gmx-users Digest, Vol 81, Issue 141
**





-Adwait


This message was sent using IMP, the Internet Messaging Program.

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Re: [gmx-users] Visualizing the simulation in VMD




bharat gupta wrote:



After running the simulation I checked the trajectory in using ngmx in 
some other system .. and it was working .. since I need to do some more 
analysis during trajectory run on my protein I thought of running into 
VMD and I used the file .trr after completng the simulation .
 



Then you probably just loaded it wrong.  Refer to a VMD tutorial.

-Justin


--
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com 



--


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] Visualizing the simulation in VMD

On Thu, Jan 20, 2011 at 7:44 PM, Justin A. Lemkul  wrote:

>
>
> bharat gupta wrote:
>
>> I loaded the .gro file generated after pdb2gmx command in vmd and then I
>> loaded the .trr file into that molecule but it shows frame 1 vol 0 in VMD
>> and when I click the play button on the toolbar the frames doesn't move ...
>> can anybody tell me how to play the simula tion in VMD ?? or where am i
>> going wrong
>>
>>
>>
> How many frames did you save in the .trr file?  Use gmxcheck.  If it has
> multiple frames, it will load them all and you can watch the movie.  Sounds
> like you haven't saved enough frames.
>
> -Justin
>
>  --
>> Bharat
>> Ph.D. Candidate
>> Room No. : 7202A, 2nd Floor
>> Biomolecular Engineering Laboratory
>> Division of Chemical Engineering and Polymer Science
>> Pusan National University
>> Busan -609735
>> South Korea
>> Lab phone no. - +82-51-510-3680, +82-51-583-8343
>> Mobile no. - 010-5818-3680
>> E-mail : monu46...@yahoo.com 
>>
>>
> --
> 
>
> 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
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>


After running the simulation I checked the trajectory in using ngmx in some
other system .. and it was working .. since I need to do some more analysis
during trajectory run on my protein I thought of running into VMD and I used
the file .trr after completng the simulation .


-- 
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com
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Re: [gmx-users] Regarding g_analyze




bharat gupta wrote:
It means that  rmsd plot is stable .. I am trying to run the trajectory 
in windows using VMD and for that i followed what was said in past 
thread of gmx discussion list but I am not able to run the trajectory 
and for that I have posted another question regarding that jus 5 mins back..
 
Also if u can shed some light of this very important issue ... that to 
learn simulation in gromacs and to analyze the things needed for our 
analysis .. what exactly do we need to do .. as in my case i am 
following ur tutorial and asking doubts in the gmx user list but I am 
not able to get many things still ... like analysing the plots and 
graphs and how to tell whch value is correct at what particular time for 
how much simulation time ?? ... pls do ket me know how can I have a firm 
grip in this regard...
 


You need to develop a set of measurable quantities that your simulation should 
address long before you even begin building the system.  Then, once you identify 
what you will measure and how you will measure it, design the simulation system 
and run the MD.  What you define as "correct" depends entirely upon what is 
being measured, what the system is, and what the question is that you're asking.


No one on this list is going to be able (or willing, usually) to help you work 
through your project, so do invest some time with textbook and literature 
reading to get a sense of what you should be doing.


-Justin



--
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com 



--


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] Regarding g_analyze

It means that  rmsd plot is stable .. I am trying to run the trajectory in
windows using VMD and for that i followed what was said in past thread of
gmx discussion list but I am not able to run the trajectory and for that I
have posted another question regarding that jus 5 mins back..

Also if u can shed some light of this very important issue ... that to learn
simulation in gromacs and to analyze the things needed for our analysis ..
what exactly do we need to do .. as in my case i am following ur tutorial
and asking doubts in the gmx user list but I am not able to get many things
still ... like analysing the plots and graphs and how to tell whch value is
correct at what particular time for how much simulation time ?? ... pls do
ket me know how can I have a firm grip in this regard...


-- 
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com
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RE: [gmx-users] Visualizing the simulation in VMD

2011-01-20 Thread Dallas Warren

This is more of a question you should be directing to the VMD emailing
list.

 

How many frames does your .trr file contain?

 

Use gmxcheck to see what the .trr file contains.

 

Catch ya,

Dr. Dallas Warren

Medicinal Chemistry and Drug Action

Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@monash.edu

+61 3 9903 9304
-
When the only tool you own is a hammer, every problem begins to resemble
a nail. 

 

From: gmx-users-boun...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org] On Behalf Of bharat gupta
Sent: Friday, 21 January 2011 2:42 PM
To: Discussion list for GROMACS users
Subject: [gmx-users] Visualizing the simulation in VMD

 

I loaded the .gro file generated after pdb2gmx command in vmd and then I
loaded the .trr file into that molecule but it shows frame 1 vol 0 in
VMD and when I click the play button on the toolbar the frames doesn't
move ... can anybody tell me how to play the simula tion in VMD ?? or
where am i going wrong



-- 
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343

Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com

 

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Re: [gmx-users] Visualizing the simulation in VMD




bharat gupta wrote:
I loaded the .gro file generated after pdb2gmx command in vmd and then I 
loaded the .trr file into that molecule but it shows frame 1 vol 0 in 
VMD and when I click the play button on the toolbar the frames doesn't 
move ... can anybody tell me how to play the simula tion in VMD ?? or 
where am i going wrong





How many frames did you save in the .trr file?  Use gmxcheck.  If it has 
multiple frames, it will load them all and you can watch the movie.  Sounds like 
you haven't saved enough frames.


-Justin


--
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com 



--


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] Regarding g_analyze




bharat gupta wrote:
 
I generated this graph using xyplot since I was not able to install 
xmgrace on windows platform .. also I want to one more thing ... that I 
calculated the rmsd and rmsd_xtal graph .. I found them to be same and 
the fluctuations in graph is same for 0 to 1.5 nm and then last  2.4 to 
3 ns .. does it mean that the structure is stable.. I have attached both 
the files and the plotted file also.. pls if possible do comment on this 
issue also..




3 ns is fairly short to conclude that anything is truly stable.  Watch the 
trajectory to see what's going on.  I see nothing obviously wrong with either 
RMSD plot.


-Justin


--
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com 



--


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] Visualizing the simulation in VMD

I loaded the .gro file generated after pdb2gmx command in vmd and then I
loaded the .trr file into that molecule but it shows frame 1 vol 0 in VMD
and when I click the play button on the toolbar the frames doesn't move ...
can anybody tell me how to play the simula tion in VMD ?? or where am i
going wrong


-- 
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com
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Re: [gmx-users] Regarding g_analyze




bharat gupta wrote:

Hi,
 
After  completing my simulation , I have generated the potential.xvg 
file and also I generated the average of the potential for the whole 
simulation using g_analyze. But when I open the file average.avg I shows 
me the same graph as that of potential.xvg but with red color.. What I 
want is a red line averaging the potential value in the potential graph 
as given in the lysozyme tutorial.




Red indicates the second data set loaded by xmgrace, which in your case sounds 
like it is identical to the first.  The running average you refer to was not 
generated by Gromacs, rather it is an xmgrace function.  Data -> Transformations 
-> Running averages.


-Justin



--
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com 



--


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] Regarding g_analyze

Hi,

After  completing my simulation , I have generated the potential.xvg file
and also I generated the average of the potential for the whole simulation
using g_analyze. But when I open the file average.avg I shows me the same
graph as that of potential.xvg but with red color.. What I want is a red
line averaging the potential value in the potential graph as given in the
lysozyme tutorial.


-- 
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com
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Re: [gmx-users] How to install a new Forcefield in Gromacs 4.5.3

Qin Qiao wrote:

2011/1/21 Justin A. Lemkul mailto:jalem...@vt.edu>>

Qin Qiao wrote:

2011/1/21 Justin A. Lemkul mailto:jalem...@vt.edu> >>

   Qin Qiao wrote:

   2011/1/20 Justin A. Lemkul mailto:jalem...@vt.edu>
   >

   >

>>

>

 Qin Qiao wrote:

 2011/1/20 Justin A. Lemkul mailto:jalem...@vt.edu>
   >

>>
  >

>

>>

  >

>

Qin Qiao wrote:

Dear all,

I would like to try a new forcefield
in Gromacs
  4.5.3. What
should I do after I copied the ff to
  /share/gromacs/top
directory? It seems the original
FF.dat doesn't
  exist in
 4.5.3..
Could you give me some help?

pdb2gmx detects forcefield directories
by searching
  for names
 that
end in .ff, then looking in that
directory for a
  "forcefield.doc"
file that contains a brief description
of the
   force field.

-Justin

 Thanks. But I cannot find the new
forcefield when
   I used
 pdb2gmx.. the folder of ff is named 'PACE.ff'

 It must also contain a forcefield.itp file to be
   recognized, and
 ultimately, to work at all.  I did a test of
minimum
  requirements,
 and only after I added a dummy forcefield.itp
file to
   the test.ff
 subdirectory did pdb2gmx recognize the new
force field.

 -Justin

  There is an .itp file in the ff.. but it doesn't
work..
  strange.. is there any other possibility?

  It works just fine for me.  To be sure, I used the
name "PACE.ff"
  instead of my generic "test.ff" to make sure
capitalization or
  something foolish wasn't a problem.  It worked fine,
adding
   "PACE"
  as entry 16 in the pdb2gmx menu (I also have another
custom force
  field, so the order of your pdb2gmx output may be
different).

  The other thing to try is to build the force field in your
   working
  directory and see if pdb2gmx finds it there.  This is,
of course,
  not strictly required (and would be very
inconvenient), but
   it could
  be a useful diagnostic.

  -Justin

   Thanks. But it doesn't work.. and I tried to copy the exact
   files in the charmm.ff to a new test.ff, and pdb2gmx doesn't

Re: [gmx-users] How to install a new Forcefield in Gromacs 4.5.3

2011/1/21 Justin A. Lemkul 

>
>
> Qin Qiao wrote:
>
>>
>>
>> 2011/1/21 Justin A. Lemkul mailto:jalem...@vt.edu>>
>>
>>
>>
>>
>>Qin Qiao wrote:
>>
>>
>>
>>2011/1/20 Justin A. Lemkul > >>>
>>
>>
>>
>>   Qin Qiao wrote:
>>
>>
>>
>>   2011/1/20 Justin A. Lemkul >
>>   >
>>
>>   >
>>
>>
>>  Qin Qiao wrote:
>>
>>
>>
>>  2011/1/20 Justin A. Lemkul >
>>   >
>>  
>>>>
>>   
>>>
>>
>>  
>>
>>
>>
>>
>>
>>
>> Qin Qiao wrote:
>>
>> Dear all,
>>
>> I would like to try a new forcefield in
>> Gromacs
>>   4.5.3. What
>> should I do after I copied the ff to
>>   /share/gromacs/top
>> directory? It seems the original FF.dat
>> doesn't
>>   exist in
>>  4.5.3..
>> Could you give me some help?
>>
>>
>> pdb2gmx detects forcefield directories by
>> searching
>>   for names
>>  that
>> end in .ff, then looking in that directory for a
>>   "forcefield.doc"
>> file that contains a brief description of the
>>force field.
>>
>> -Justin
>>
>>
>>  Thanks. But I cannot find the new forcefield when
>>I used
>>  pdb2gmx.. the folder of ff is named 'PACE.ff'
>>
>>
>>  It must also contain a forcefield.itp file to be
>>recognized, and
>>  ultimately, to work at all.  I did a test of minimum
>>   requirements,
>>  and only after I added a dummy forcefield.itp file to
>>the test.ff
>>  subdirectory did pdb2gmx recognize the new force field.
>>
>>  -Justin
>>
>>
>>   There is an .itp file in the ff.. but it doesn't work..
>>   strange.. is there any other possibility?
>>
>>
>>   It works just fine for me.  To be sure, I used the name
>> "PACE.ff"
>>   instead of my generic "test.ff" to make sure capitalization or
>>   something foolish wasn't a problem.  It worked fine, adding
>>"PACE"
>>   as entry 16 in the pdb2gmx menu (I also have another custom
>> force
>>   field, so the order of your pdb2gmx output may be different).
>>
>>   The other thing to try is to build the force field in your
>>working
>>   directory and see if pdb2gmx finds it there.  This is, of
>> course,
>>   not strictly required (and would be very inconvenient), but
>>it could
>>   be a useful diagnostic.
>>
>>   -Justin
>>
>>
>>Thanks. But it doesn't work.. and I tried to copy the exact
>>files in the charmm.ff to a new test.ff, and pdb2gmx doesn't
>>find test.ff..
>>
>>
>>Do you have multiple versions of Gromacs on the same machine?  If
>>so, are you calling the right pdb2gmx?
>>
>> Could you tell me how can I tell which version of pdb2gmx I call?
>>
>>
> pdb2gmx -h
>
> -Justin
>
>
> Thanks. The version is 4.5.1, but it just doesn't work.

> --
> 
>
> 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
>
-- 
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http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
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Please don't post (un)s

Re: [gmx-users] How to install a new Forcefield in Gromacs 4.5.3

Qin Qiao wrote:

2011/1/21 Justin A. Lemkul mailto:jalem...@vt.edu>>

Qin Qiao wrote:

2011/1/20 Justin A. Lemkul mailto:jalem...@vt.edu> >>

   Qin Qiao wrote:

   2011/1/20 Justin A. Lemkul mailto:jalem...@vt.edu>
   >

   >

>>

>

 Qin Qiao wrote:

 Dear all,

 I would like to try a new forcefield in Gromacs
   4.5.3. What
 should I do after I copied the ff to
   /share/gromacs/top
 directory? It seems the original FF.dat doesn't
   exist in
  4.5.3..
 Could you give me some help?

 pdb2gmx detects forcefield directories by searching
   for names
  that
 end in .ff, then looking in that directory for a
   "forcefield.doc"
 file that contains a brief description of the
force field.

 -Justin

  Thanks. But I cannot find the new forcefield when
I used
  pdb2gmx.. the folder of ff is named 'PACE.ff'

  It must also contain a forcefield.itp file to be
recognized, and
  ultimately, to work at all.  I did a test of minimum
   requirements,
  and only after I added a dummy forcefield.itp file to
the test.ff
  subdirectory did pdb2gmx recognize the new force field.

  -Justin

   There is an .itp file in the ff.. but it doesn't work..
   strange.. is there any other possibility?

   It works just fine for me.  To be sure, I used the name "PACE.ff"
   instead of my generic "test.ff" to make sure capitalization or
   something foolish wasn't a problem.  It worked fine, adding
"PACE"
   as entry 16 in the pdb2gmx menu (I also have another custom force
   field, so the order of your pdb2gmx output may be different).

   The other thing to try is to build the force field in your
working
   directory and see if pdb2gmx finds it there.  This is, of course,
   not strictly required (and would be very inconvenient), but
it could
   be a useful diagnostic.

   -Justin

Thanks. But it doesn't work.. and I tried to copy the exact
files in the charmm.ff to a new test.ff, and pdb2gmx doesn't
find test.ff..

Do you have multiple versions of Gromacs on the same machine?  If
so, are you calling the right pdb2gmx?

Could you tell me how can I tell which version of pdb2gmx I call?

pdb2gmx -h

-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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Please search the archive at 
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Re: [gmx-users] How to install a new Forcefield in Gromacs 4.5.3

2011/1/21 Justin A. Lemkul 

>
>
> Qin Qiao wrote:
>
>>
>>
>> 2011/1/20 Justin A. Lemkul mailto:jalem...@vt.edu>>
>>
>>
>>
>>Qin Qiao wrote:
>>
>>
>>
>>2011/1/20 Justin A. Lemkul > >>>
>>
>>
>>
>>   Qin Qiao wrote:
>>
>>
>>
>>   2011/1/20 Justin A. Lemkul >
>>   >
>>
>>
>>   >
>>
>>
>>
>>
>>  Qin Qiao wrote:
>>
>>  Dear all,
>>
>>  I would like to try a new forcefield in Gromacs
>>4.5.3. What
>>  should I do after I copied the ff to
>>/share/gromacs/top
>>  directory? It seems the original FF.dat doesn't
>>exist in
>>   4.5.3..
>>  Could you give me some help?
>>
>>
>>  pdb2gmx detects forcefield directories by searching
>>for names
>>   that
>>  end in .ff, then looking in that directory for a
>>"forcefield.doc"
>>  file that contains a brief description of the force
>> field.
>>
>>  -Justin
>>
>>
>>   Thanks. But I cannot find the new forcefield when I used
>>   pdb2gmx.. the folder of ff is named 'PACE.ff'
>>
>>
>>   It must also contain a forcefield.itp file to be recognized, and
>>   ultimately, to work at all.  I did a test of minimum
>>requirements,
>>   and only after I added a dummy forcefield.itp file to the
>> test.ff
>>   subdirectory did pdb2gmx recognize the new force field.
>>
>>   -Justin
>>
>>
>>There is an .itp file in the ff.. but it doesn't work..
>>strange.. is there any other possibility?
>>
>>
>>It works just fine for me.  To be sure, I used the name "PACE.ff"
>>instead of my generic "test.ff" to make sure capitalization or
>>something foolish wasn't a problem.  It worked fine, adding "PACE"
>>as entry 16 in the pdb2gmx menu (I also have another custom force
>>field, so the order of your pdb2gmx output may be different).
>>
>>The other thing to try is to build the force field in your working
>>directory and see if pdb2gmx finds it there.  This is, of course,
>>not strictly required (and would be very inconvenient), but it could
>>be a useful diagnostic.
>>
>>-Justin
>>
>>
>> Thanks. But it doesn't work.. and I tried to copy the exact files in the
>> charmm.ff to a new test.ff, and pdb2gmx doesn't find test.ff..
>>
>>
> Do you have multiple versions of Gromacs on the same machine?  If so, are
> you calling the right pdb2gmx?
>
> Could you tell me how can I tell which version of pdb2gmx I call?


-Justin
>
>
>
>>  Best,
>>
>>  Qin
>>
>>
>>  -- 
>>
>>  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/Searchbefore
>>   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
>>

Re: [gmx-users] How to install a new Forcefield in Gromacs 4.5.3

In the first instance of creating a new forcefield, do so in your 
working directory - create myforcefield.ff directory and fill it with 
your fields. pdb2gmx 4.5.x will find this and let you use it according 
to the name in forcefield.doc (IIRC). Once you have it working properly, 
then consider installing this in the $GMXLIB folder for future convenience


Mark
--
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Re: [gmx-users] How to install a new Forcefield in Gromacs 4.5.3

Qin Qiao wrote:

2011/1/20 Justin A. Lemkul mailto:jalem...@vt.edu>>

Qin Qiao wrote:

2011/1/20 Justin A. Lemkul mailto:jalem...@vt.edu> >>

   Qin Qiao wrote:

   2011/1/20 Justin A. Lemkul mailto:jalem...@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

   -- 

   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 mailin

Re: [gmx-users] How to install a new Forcefield in Gromacs 4.5.3

2011/1/20 Justin A. Lemkul 

>
>
> Qin Qiao wrote:
>
>>
>>
>> 2011/1/20 Justin A. Lemkul mailto:jalem...@vt.edu>>
>>
>>
>>
>>Qin Qiao wrote:
>>
>>
>>
>>2011/1/20 Justin A. Lemkul > >
>>>>
>>
>>
>>
>>
>>   Qin Qiao wrote:
>>
>>   Dear all,
>>
>>   I would like to try a new forcefield in Gromacs 4.5.3. What
>>   should I do after I copied the ff to /share/gromacs/top
>>   directory? It seems the original FF.dat doesn't exist in
>>4.5.3..
>>   Could you give me some help?
>>
>>
>>   pdb2gmx detects forcefield directories by searching for names
>>that
>>   end in .ff, then looking in that directory for a
>> "forcefield.doc"
>>   file that contains a brief description of the force field.
>>
>>   -Justin
>>
>>
>>Thanks. But I cannot find the new forcefield when I used
>>pdb2gmx.. the folder of ff is named 'PACE.ff'
>>
>>
>>It must also contain a forcefield.itp file to be recognized, and
>>ultimately, to work at all.  I did a test of minimum requirements,
>>and only after I added a dummy forcefield.itp file to the test.ff
>>subdirectory did pdb2gmx recognize the new force field.
>>
>>-Justin
>>
>>
>> There is an .itp file in the ff.. but it doesn't work.. strange.. is there
>> any other possibility?
>>
>>
> It works just fine for me.  To be sure, I used the name "PACE.ff" instead
> of my generic "test.ff" to make sure capitalization or something foolish
> wasn't a problem.  It worked fine, adding "PACE" as entry 16 in the pdb2gmx
> menu (I also have another custom force field, so the order of your pdb2gmx
> output may be different).
>
> The other thing to try is to build the force field in your working
> directory and see if pdb2gmx finds it there.  This is, of course, not
> strictly required (and would be very inconvenient), but it could be a useful
> diagnostic.
>
> -Justin
>
>
>> Thanks. But it doesn't work.. and I tried to copy the exact files in the
charmm.ff to a new test.ff, and pdb2gmx doesn't find test.ff..



>   Best,
>>
>>   Qin
>>
>>
>>   -- 
>>
>>   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
>>
>>
>>
>>-- 
>>
>>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
>>
>>
>>
> --
> 
>
> 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 p

Re: [gmx-users] Running a crashed run




bharat gupta wrote:

Hi,
 
I am running a crashed run (orgininally for a 3ns simulation) but at the 
time of rerunning I forgot to assign -v tag in the command and now I an 
not able to know at which step the simulation is going on .. For that I 
check the state.cpt file , actually there are two .cpt files one with 
state.cpt and other with state_prev.cpt (this one got created while 
rerunning the simulation) in one file its showing last frame as 926 and 
other file as 924 so I don't know at what step the simulation is going 
on (originally I kept for 150 steps). Can anybody let me know how to 
find out at what time is this simulation going on ??
 



This simulation picks up from whichever .cpt file you told mdrun to use.  If you 
want to know where in the simulation you are, use the "tail" command to have a 
look at your .log file.


-Justin



--
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com 



--


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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http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
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[gmx-users] Running a crashed run

Hi,

I am running a crashed run (orgininally for a 3ns simulation) but at the
time of rerunning I forgot to assign -v tag in the command and now I an not
able to know at which step the simulation is going on .. For that I check
the state.cpt file , actually there are two .cpt files one with state.cpt
and other with state_prev.cpt (this one got created while rerunning the
simulation) in one file its showing last frame as 926 and other file as 924
so I don't know at what step the simulation is going on (originally I kept
for 150 steps). Can anybody let me know how to find out at what time is
this simulation going on ??



-- 
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com
-- 
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[gmx-users] Problem with using topolbuild1_3.tgz

2011-01-20 Thread Sweta Iyer

Hi, I am trying to generate topology files for a set of lipids with the
help of topolbuild1_3.tgz package found at the other software page of
GROMACS website.

I downloaded and installed all files and tried running the program with a
MOL2 file with charges in it. However, it shows an error message as
follows:

Fatal error.
Source code file: readmol2.c, line: 758
Atom 1 (C) has 3 connections when allowed 0

 I am not sure how to get over this problem! Wonder what will fix this
error and get the program running!

Thanx



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Re: [gmx-users] Inaccurate pressure readings


On 21/01/2011 10:12 AM, Denny Frost wrote:
Sorry, I'm referring to a lot of runs here - some fluctuate more than 
others and some have greater average values than others.  The average 
value is never greater than the maximum fluctuation in each run, so 
that is not a problem.  The average given by g_energy, however, is not 
close to 1.0 bar in any of my runs.  Some runs give an average 
pressure of 10 bar, some give an average value of -1000 bar.


In addition to all the points Justin mentioned, I'd observe that you're 
generating velocities at the start of the run, so the system will not be 
equilibrated for some time after that. See the advice here 
www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation. 
Anyway, you don't want to collect data for averages until after 
equilibration.


Secondly, tau-t of 0.1 is useful for equilibration, but a bit too 
stringent for actual simulations. Using v-rescale T-coupling is probably 
a good idea too.


Until you address all these issues about the numerical quality of your 
model of reality, hoping for observables to correlate with reality is 
not justified.


Mark



On Thu, Jan 20, 2011 at 3:51 PM, Dallas Warren 
mailto:dallas.war...@monash.edu>> wrote:


Then something you have said isn’t right.  In first email you said
that the pressure varies between -400 and +400 bar.  Now you say
that the average can vary from -1000 to +1000 bar.  If the
instantaneous pressure is varying from -1000 to +1000 bar, then
that is not a real issue.  However, if the average can be from
-1000 to +1000 bar, then that definitely is.


Which one is it?

Catch ya,

Dr. Dallas Warren

Medicinal Chemistry and Drug Action

Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@monash.edu 

+61 3 9903 9304
-
When the only tool you own is a hammer, every problem begins to
resemble a nail.

*From:*gmx-users-boun...@gromacs.org

[mailto:gmx-users-boun...@gromacs.org
] *On Behalf Of *Denny Frost
*Sent:* Friday, 21 January 2011 9:23 AM
*To:* Discussion list for GROMACS users
*Subject:* Re: [gmx-users] Inaccurate pressure readings

The average I calculate is not within -10 to 10, it is on the
order of -1000 to 1000

On Thu, Jan 20, 2011 at 3:11 PM, Dallas Warren
mailto:dallas.war...@monash.edu>> wrote:

You have a variable that is fluctuating over a range of 800+ units
(three orders of magnitude) and want the average to be 1.0?

It is not a problem as such.  If you can get a large enough data
set of pressure data, and it will have to be very large, then you
might get it close to one.

But as long the average you calculate is within may be an order of
magnitude (-10 to 10) then there is nothing to get too worried about.

Catch ya,

Dr. Dallas Warren

Medicinal Chemistry and Drug Action

Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@monash.edu 

+61 3 9903 9304
-
When the only tool you own is a hammer, every problem begins to
resemble a nail.

*From:*gmx-users-boun...@gromacs.org

[mailto:gmx-users-boun...@gromacs.org
] *On Behalf Of *Denny Frost
*Sent:* Friday, 21 January 2011 9:07 AM
*To:* gmx-users@gromacs.org 
*Subject:* [gmx-users] Inaccurate pressure readings

I am running a variety of NPT simulations with polar, non-polar,
and ionic compounds.  Although my results for density agree well
with experimental values, the pressures I get from g_energy are
off by 1 to 3 orders of magnitude.  In the log file, the pressure
fluctuates around a lot from -400 to 400 bar, which seems to be
normal according to other posts on this list, but the average
(which is what g_energy gives me) is not 1.0 bar, as I specified.
 Does anyone know how to correct this problem?

Pressure coupling parameters:

Pcoupl  =  berendsen

pcoupltype  =  isotropic

tau_p   =  1.0

ref_p   =  1.0

compressibility =  4.5e-5


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Re: [gmx-users] Inaccurate pressure readings

Sorry, I'm referring to a lot of runs here - some fluctuate more than others
and some have greater average values than others.  The average value is
never greater than the maximum fluctuation in each run, so that is not a
problem.  The average given by g_energy, however, is not close to 1.0 bar in
any of my runs.  Some runs give an average pressure of 10 bar, some give an
average value of -1000 bar.

On Thu, Jan 20, 2011 at 3:51 PM, Dallas Warren wrote:

> Then something you have said isn’t right.  In first email you said that the
> pressure varies between -400 and +400 bar.  Now you say that the average can
> vary from -1000 to +1000 bar.  If the instantaneous pressure is varying from
> -1000 to +1000 bar, then that is not a real issue.  However, if the average
> can be from -1000 to +1000 bar, then that definitely is.
>
>
> Which one is it?
>
>
>
> Catch ya,
>
> Dr. Dallas Warren
>
> Medicinal Chemistry and Drug Action
>
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3010
> dallas.war...@monash.edu
>
> +61 3 9903 9304
> -
> When the only tool you own is a hammer, every problem begins to resemble a
> nail.
>
>
>
> *From:* gmx-users-boun...@gromacs.org [mailto:
> gmx-users-boun...@gromacs.org] *On Behalf Of *Denny Frost
> *Sent:* Friday, 21 January 2011 9:23 AM
> *To:* Discussion list for GROMACS users
> *Subject:* Re: [gmx-users] Inaccurate pressure readings
>
>
>
> The average I calculate is not within -10 to 10, it is on the order of
> -1000 to 1000
>
> On Thu, Jan 20, 2011 at 3:11 PM, Dallas Warren 
> wrote:
>
> You have a variable that is fluctuating over a range of 800+ units (three
> orders of magnitude) and want the average to be 1.0?
>
>
>
> It is not a problem as such.  If you can get a large enough data set of
> pressure data, and it will have to be very large, then you might get it
> close to one.
>
>
>
> But as long the average you calculate is within may be an order of
> magnitude (-10 to 10) then there is nothing to get too worried about.
>
>
>
> Catch ya,
>
> Dr. Dallas Warren
>
> Medicinal Chemistry and Drug Action
>
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3010
> dallas.war...@monash.edu
>
> +61 3 9903 9304
> -
> When the only tool you own is a hammer, every problem begins to resemble a
> nail.
>
>
>
> *From:* gmx-users-boun...@gromacs.org [mailto:
> gmx-users-boun...@gromacs.org] *On Behalf Of *Denny Frost
> *Sent:* Friday, 21 January 2011 9:07 AM
> *To:* gmx-users@gromacs.org
> *Subject:* [gmx-users] Inaccurate pressure readings
>
>
>
> I am running a variety of NPT simulations with polar, non-polar, and ionic
> compounds.  Although my results for density agree well with experimental
> values, the pressures I get from g_energy are off by 1 to 3 orders of
> magnitude.  In the log file, the pressure fluctuates around a lot from -400
> to 400 bar, which seems to be normal according to other posts on this list,
> but the average (which is what g_energy gives me) is not 1.0 bar, as I
> specified.  Does anyone know how to correct this problem?
>
>
>
> Pressure coupling parameters:
>
> Pcoupl  =  berendsen
>
> pcoupltype  =  isotropic
>
> tau_p   =  1.0
>
> ref_p   =  1.0
>
> compressibility =  4.5e-5
>
>
> --
>
> 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
>
>
>
> --
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Re: [gmx-users] Inaccurate pressure readings

Denny Frost wrote:
Sorry about forgetting the simulation time.  They run for about 12 ns, 
at which point I stop them.  They appear stable - the box vectors don't 
change a lot (which is surprising since the pressure sure does).  Below 
is a complete mdp file.

If the box vectors aren't changing, then it's very odd that the pressure is not 
a more acceptable value.  What of the other parameters - temperature, energy, 
etc?  What type of energy minimization and/or equilibration did you do prior to 
this run?

A few other notes:

title = Run1
cpp =  /lib/cpp
constraints =  all_bonds
integrator  =  md
dt  =  0.004   ; ps !

Are you using virtual sites?  If not, a 4-fs timestep may not be stable, even 
with constraints.

nsteps  =  2000   ; total 4ns.
nstcomm =  1
nstxout =  5
nstvout =  5
nstfout =  0
nstlog  =  5000
nstenergy   =  5000
nstxtcout   =  25000
nstlist =  10
ns_type =  grid
pbc =  xyz
coulombtype =  PME
vdwtype =  Shift
rlist   =  1.0
rcoulomb=  1.0
rvdw=  1.0
fourierspacing  =  0.6

This fourierspacing is 5-6 times larger than what is generally considered 
sufficiently accurate.  Your PME term may be inaccurate if there are 
insufficient grid points.  If you're increasing the spacing for performance 
reasons, you may be sacrificing accuracy.

;pme_order   =  4
ewald_rtol  =  1e-5
; Berendsen temperature coupling is on in two groups
Tcoupl  =  berendsen
tc_grps =  BMI  PF6  

Are both of these groups large enough to warrant their own temperature coupling 
groups?

http://www.gromacs.org/Documentation/Terminology/Thermostats

-Justin

tau_t   =  0.1  0.1
ref_t   =  300  300
nsttcouple  =  1
; Energy monitoring
energygrps  =  BMI  PF6
; Isotropic pressure coupling is now on
Pcoupl  =  berendsen
pcoupltype  =  isotropic
;pc-grps =  BMI  PFF
tau_p   =  1.0
ref_p   =  1.0
compressibility =  4.5e-5

; Generate velocites is off at 300 K.
gen_vel =  yes
gen_temp=  300.0
gen_seed=  10

On Thu, Jan 20, 2011 at 3:49 PM, Justin A. Lemkul > wrote:

Denny Frost wrote:

from -1000 to 1000, depending on the system.  The simulation box
is 8x8x8 nm (roughly) and contains about 12,000 atoms

Are the systems even stable?  Is there a trend in the pressure, or
is it stable at those values?  It seems that the systems are either
exploding or imploding. How long are the simulations?  Can you post
a complete .mdp file?

-Justin

On Thu, Jan 20, 2011 at 3:09 PM, Justin A. Lemkul
mailto:jalem...@vt.edu>
>> wrote:

   Denny Frost wrote:

   I am running a variety of NPT simulations with polar,
non-polar,
   and ionic compounds.  Although my results for density
agree well
   with experimental values, the pressures I get from
g_energy are
   off by 1 to 3 orders of magnitude.  In the log file, the
   pressure fluctuates around a lot from -400 to 400 bar, which
   seems to be normal according to other posts on this list, but
   the average (which is what g_energy gives me) is not 1.0
bar, as
   I specified.  Does anyone know how to correct this problem?

   What is the average value you're getting?  How long are your
   simulations?

   -Justin

   Pressure coupling parameters:
   Pcoupl  =  berendsen
   pcoupltype  =  isotropic
   tau_p   =  1.0
   ref_p   =  1.0
   compressibility =  4.5e-5

   -- 

   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
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posting!

Re: [gmx-users] Inaccurate pressure readings

2011-01-20 Thread Warren Gallin

This seems odd.

If a value fluctuates between -400 and +400, how can the average be outside the 
range?

Warren Gallin

On 2011-01-20, at 3:24 PM, Denny Frost wrote:

> from -1000 to 1000, depending on the system.  The simulation box is 8x8x8 nm 
> (roughly) and contains about 12,000 atoms
> 
> On Thu, Jan 20, 2011 at 3:09 PM, Justin A. Lemkul  wrote:
> 
> 
> Denny Frost wrote:
> I am running a variety of NPT simulations with polar, non-polar, and ionic 
> compounds.  Although my results for density agree well with experimental 
> values, the pressures I get from g_energy are off by 1 to 3 orders of 
> magnitude.  In the log file, the pressure fluctuates around a lot from -400 
> to 400 bar, which seems to be normal according to other posts on this list, 
> but the average (which is what g_energy gives me) is not 1.0 bar, as I 
> specified.  Does anyone know how to correct this problem?
> 
> 
> What is the average value you're getting?  How long are your simulations?
> 
> -Justin
> 
> 
> Pressure coupling parameters:
> Pcoupl  =  berendsen
> pcoupltype  =  isotropic
> tau_p   =  1.0
> ref_p   =  1.0
> compressibility =  4.5e-5
> 
> 
> -- 
> 
> 
> 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!
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> 
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RE: [gmx-users] Inaccurate pressure readings

2011-01-20 Thread Dallas Warren

Then something you have said isn't right.  In first email you said that
the pressure varies between -400 and +400 bar.  Now you say that the
average can vary from -1000 to +1000 bar.  If the instantaneous pressure
is varying from -1000 to +1000 bar, then that is not a real issue.
However, if the average can be from -1000 to +1000 bar, then that
definitely is.


Which one is it?

 

Catch ya,

Dr. Dallas Warren

Medicinal Chemistry and Drug Action

Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@monash.edu

+61 3 9903 9304
-
When the only tool you own is a hammer, every problem begins to resemble
a nail. 

 

From: gmx-users-boun...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org] On Behalf Of Denny Frost
Sent: Friday, 21 January 2011 9:23 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Inaccurate pressure readings

 

The average I calculate is not within -10 to 10, it is on the order of
-1000 to 1000

On Thu, Jan 20, 2011 at 3:11 PM, Dallas Warren
 wrote:

You have a variable that is fluctuating over a range of 800+ units
(three orders of magnitude) and want the average to be 1.0?

 

It is not a problem as such.  If you can get a large enough data set of
pressure data, and it will have to be very large, then you might get it
close to one.

 

But as long the average you calculate is within may be an order of
magnitude (-10 to 10) then there is nothing to get too worried about.

 

Catch ya,

Dr. Dallas Warren

Medicinal Chemistry and Drug Action

Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@monash.edu

+61 3 9903 9304
-
When the only tool you own is a hammer, every problem begins to resemble
a nail. 

 

From: gmx-users-boun...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org] On Behalf Of Denny Frost
Sent: Friday, 21 January 2011 9:07 AM
To: gmx-users@gromacs.org
Subject: [gmx-users] Inaccurate pressure readings

 

I am running a variety of NPT simulations with polar, non-polar, and
ionic compounds.  Although my results for density agree well with
experimental values, the pressures I get from g_energy are off by 1 to 3
orders of magnitude.  In the log file, the pressure fluctuates around a
lot from -400 to 400 bar, which seems to be normal according to other
posts on this list, but the average (which is what g_energy gives me) is
not 1.0 bar, as I specified.  Does anyone know how to correct this
problem?

 

Pressure coupling parameters:

Pcoupl  =  berendsen

pcoupltype  =  isotropic

tau_p   =  1.0

ref_p   =  1.0

compressibility =  4.5e-5


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Re: [gmx-users] Inaccurate pressure readings

Sorry about forgetting the simulation time.  They run for about 12 ns, at
which point I stop them.  They appear stable - the box vectors don't change
a lot (which is surprising since the pressure sure does).  Below is a
complete mdp file.

title = Run1
cpp =  /lib/cpp
constraints =  all_bonds
integrator  =  md
dt  =  0.004   ; ps !
nsteps  =  2000   ; total 4ns.
nstcomm =  1
nstxout =  5
nstvout =  5
nstfout =  0
nstlog  =  5000
nstenergy   =  5000
nstxtcout   =  25000
nstlist =  10
ns_type =  grid
pbc =  xyz
coulombtype =  PME
vdwtype =  Shift
rlist   =  1.0
rcoulomb=  1.0
rvdw=  1.0
fourierspacing  =  0.6
;pme_order   =  4
ewald_rtol  =  1e-5
; Berendsen temperature coupling is on in two groups
Tcoupl  =  berendsen
tc_grps =  BMI  PF6
tau_t   =  0.1  0.1
ref_t   =  300  300
nsttcouple  =  1
; Energy monitoring
energygrps  =  BMI  PF6
; Isotropic pressure coupling is now on
Pcoupl  =  berendsen
pcoupltype  =  isotropic
;pc-grps =  BMI  PFF
tau_p   =  1.0
ref_p   =  1.0
compressibility =  4.5e-5

; Generate velocites is off at 300 K.
gen_vel =  yes
gen_temp=  300.0
gen_seed=  10


On Thu, Jan 20, 2011 at 3:49 PM, Justin A. Lemkul  wrote:

>
>
> Denny Frost wrote:
>
>> from -1000 to 1000, depending on the system.  The simulation box is 8x8x8
>> nm (roughly) and contains about 12,000 atoms
>>
>>
> Are the systems even stable?  Is there a trend in the pressure, or is it
> stable at those values?  It seems that the systems are either exploding or
> imploding. How long are the simulations?  Can you post a complete .mdp file?
>
> -Justin
>
>  On Thu, Jan 20, 2011 at 3:09 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>Denny Frost wrote:
>>
>>I am running a variety of NPT simulations with polar, non-polar,
>>and ionic compounds.  Although my results for density agree well
>>with experimental values, the pressures I get from g_energy are
>>off by 1 to 3 orders of magnitude.  In the log file, the
>>pressure fluctuates around a lot from -400 to 400 bar, which
>>seems to be normal according to other posts on this list, but
>>the average (which is what g_energy gives me) is not 1.0 bar, as
>>I specified.  Does anyone know how to correct this problem?
>>
>>
>>What is the average value you're getting?  How long are your
>>simulations?
>>
>>-Justin
>>
>>
>>Pressure coupling parameters:
>>Pcoupl  =  berendsen
>>pcoupltype  =  isotropic
>>tau_p   =  1.0
>>ref_p   =  1.0
>>compressibility =  4.5e-5
>>
>>
>>-- 
>>
>>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
>>
>>
>>
> --
> 
>
> 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] non-integer charge in a protein setup using pdb2gmx AND slow simulations in vacuum v. 4.5.3

maria goranovic wrote:
Gee. My mistake then. I did not realize the difference between -COO and 
Zwitterion_COO-.

However, when I use the zwitterion termini on both ends of the other 
chain, the total charge is 4.010, which is also *slightly*´ disturbing. 
I have seen numbers like 2.99, which are still better. Is 4.010 
acceptable within rounding off errors?

Nothing greater than 0.0001 or so should be considered a rounding problem.  With 
0.01, you have another problem.

-Justin

thank you for helping

-Maria

On Thu, Jan 20, 2011 at 2:00 PM, Justin A. Lemkul > wrote:

maria goranovic wrote:

I did use -ter and chose -COO and NH3+. Am i supposed to chose
Zwitterion_COO- and Zwitterion_NH3+ ?

That's what I said, and that's what you have, isn't it?  A single
amino acid that should have both its termini charged?

-Justin

On Thu, Jan 20, 2011 at 12:55 PM, Justin A. Lemkul
mailto:jalem...@vt.edu>
>> wrote:

   maria goranovic wrote:

   Hi

   I have figured out the vacuum slow problem. It turns out
I was
   using PBC in vacuum with PME. It is now fixed.

   The other problem is still there. My protein has 2
chains. one
   chain is simply a glutamate residue. Its charge (both
terminii
   charged is -1.11 instead of -1). here is the section of the
   topology with the charges. Why does pdb2gmx assign a
charge of
   -1.11 instead of -1 if there is a free glutamate molecule
with
   NH3+ and COO- at the terminii ?

   You're not choosing the termini correctly.  Use -ter with pdb2gmx
   and select the zwitterion forms of both termini.

   -Justin

   1   opls_287484GLU  N  1   -0.3  
14.0067   ; qtot -0.3
   2   opls_290484GLU H1  1   0.33  
  1.008   ; qtot 0.03
   3   opls_290484GLU H2  1   0.33  
  1.008   ; qtot 0.36
   4   opls_290484GLU H3  1   0.33  
  1.008   ; qtot 0.69
   5   opls_283484GLU CA  1   0.04  
 12.011   ; qtot 0.73
   6   opls_140484GLU HA  1   0.06  
  1.008   ; qtot 0.79
   7   opls_136484GLU CB  2  -0.12  
 12.011   ; qtot 0.67
   8   opls_140484GLUHB1  2   0.06  
  1.008   ; qtot 0.73
   9   opls_140484GLUHB2  2   0.06  
  1.008   ; qtot 0.79
  10   opls_274484GLU CG  3  -0.22  
 12.011   ; qtot 0.57
  11   opls_140484GLUHG1  3   0.06  
  1.008   ; qtot 0.63
  12   opls_140484GLUHG2  3   0.06  
  1.008   ; qtot 0.69
  13   opls_271484GLU CD  40.7  
 12.011   ; qtot 1.39
  14   opls_272484GLUOE1  4   -0.8  
15.9994   ; qtot 0.59
  15   opls_272484GLUOE2  4   -0.8  
15.9994   ; qtot -0.21
  16   opls_271484GLU  C  50.7  
 12.011   ; qtot 0.49
  17   opls_272484GLU O1  5   -0.8  
15.9994   ; qtot -0.31
  18   opls_272484GLU O2  5   -0.8  
15.9994   ; qtot -1.11

   On Thu, Jan 20, 2011 at 11:55 AM, Mark Abraham
   mailto:mark.abra...@anu.edu.au>
>

   >

Re: [gmx-users] Inaccurate pressure readings




Denny Frost wrote:
from -1000 to 1000, depending on the system.  The simulation box is 
8x8x8 nm (roughly) and contains about 12,000 atoms




Are the systems even stable?  Is there a trend in the pressure, or is it stable 
at those values?  It seems that the systems are either exploding or imploding. 
How long are the simulations?  Can you post a complete .mdp file?


-Justin

On Thu, Jan 20, 2011 at 3:09 PM, Justin A. Lemkul > wrote:




Denny Frost wrote:

I am running a variety of NPT simulations with polar, non-polar,
and ionic compounds.  Although my results for density agree well
with experimental values, the pressures I get from g_energy are
off by 1 to 3 orders of magnitude.  In the log file, the
pressure fluctuates around a lot from -400 to 400 bar, which
seems to be normal according to other posts on this list, but
the average (which is what g_energy gives me) is not 1.0 bar, as
I specified.  Does anyone know how to correct this problem?


What is the average value you're getting?  How long are your
simulations?

-Justin


Pressure coupling parameters:
Pcoupl  =  berendsen
pcoupltype  =  isotropic
tau_p   =  1.0
ref_p   =  1.0
compressibility =  4.5e-5


-- 



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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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] non-integer charge in a protein setup using pdb2gmx AND slow simulations in vacuum v. 4.5.3

Gee. My mistake then. I did not realize the difference between -COO and
Zwitterion_COO-.

However, when I use the zwitterion termini on both ends of the other chain,
the total charge is 4.010, which is also *slightly*´ disturbing. I have seen
numbers like 2.99, which are still better. Is 4.010 acceptable within
rounding off errors?

thank you for helping

-Maria

On Thu, Jan 20, 2011 at 2:00 PM, Justin A. Lemkul  wrote:

>
>
> maria goranovic wrote:
>
>> I did use -ter and chose -COO and NH3+. Am i supposed to chose
>> Zwitterion_COO- and Zwitterion_NH3+ ?
>>
>
> That's what I said, and that's what you have, isn't it?  A single amino
> acid that should have both its termini charged?
>
> -Justin
>
>  On Thu, Jan 20, 2011 at 12:55 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>maria goranovic wrote:
>>
>>Hi
>>
>>I have figured out the vacuum slow problem. It turns out I was
>>using PBC in vacuum with PME. It is now fixed.
>>
>>The other problem is still there. My protein has 2 chains. one
>>chain is simply a glutamate residue. Its charge (both terminii
>>charged is -1.11 instead of -1). here is the section of the
>>topology with the charges. Why does pdb2gmx assign a charge of
>>-1.11 instead of -1 if there is a free glutamate molecule with
>>NH3+ and COO- at the terminii ?
>>
>>
>>You're not choosing the termini correctly.  Use -ter with pdb2gmx
>>and select the zwitterion forms of both termini.
>>
>>-Justin
>>
>>
>>1   opls_287484GLU  N  1   -0.3
>> 14.0067   ; qtot -0.3
>>2   opls_290484GLU H1  1   0.33
>> 1.008   ; qtot 0.03
>>3   opls_290484GLU H2  1   0.33
>> 1.008   ; qtot 0.36
>>4   opls_290484GLU H3  1   0.33
>> 1.008   ; qtot 0.69
>>5   opls_283484GLU CA  1   0.04
>>  12.011   ; qtot 0.73
>>6   opls_140484GLU HA  1   0.06
>> 1.008   ; qtot 0.79
>>7   opls_136484GLU CB  2  -0.12
>>  12.011   ; qtot 0.67
>>8   opls_140484GLUHB1  2   0.06
>> 1.008   ; qtot 0.73
>>9   opls_140484GLUHB2  2   0.06
>> 1.008   ; qtot 0.79
>>   10   opls_274484GLU CG  3  -0.22
>>  12.011   ; qtot 0.57
>>   11   opls_140484GLUHG1  3   0.06
>> 1.008   ; qtot 0.63
>>   12   opls_140484GLUHG2  3   0.06
>> 1.008   ; qtot 0.69
>>   13   opls_271484GLU CD  40.7
>>  12.011   ; qtot 1.39
>>   14   opls_272484GLUOE1  4   -0.8
>> 15.9994   ; qtot 0.59
>>   15   opls_272484GLUOE2  4   -0.8
>> 15.9994   ; qtot -0.21
>>   16   opls_271484GLU  C  50.7
>>  12.011   ; qtot 0.49
>>   17   opls_272484GLU O1  5   -0.8
>> 15.9994   ; qtot -0.31
>>   18   opls_272484GLU O2  5   -0.8
>> 15.9994   ; qtot -1.11
>>
>>
>>
>>On Thu, Jan 20, 2011 at 11:55 AM, Mark Abraham
>>mailto:mark.abra...@anu.edu.au>
>>>>> wrote:
>>
>>
>>
>>   On 01/20/11, *maria goranovic * >
>>   >
>>>> wrote:
>>
>>   Hi
>>
>>   I have a protein whose topology I built using pdb2gmx
>>with the -ss
>>   option and the opls-aa force field. When I run grompp,
>>the total
>>   charge on the protein is reported as 2.9 (not 2.999). Why a
>>   non-zero charge? Does this have something to do with the
>>disulfide
>>   bridge?
>>
>>
>>   Something is materially wrong, like mangled termini. Have a
>>look at
>>   the resulting structure.
>>
>>
>>   Secondly, when I run a simulation of the same protein
>>(7000 atoms)
>>   with certain restraints in vacuum, the simulation runs
>>very slow.
>>   I am wondering why. I am not using particle
>>decomposition. the box
>>   size is 50 x 50 x 50 nm. Using 4.5.3
>>
>>
>>   Have a look at the end of the .log file for some performance
>>data.
>>   How are you assessing "very slow"?
>>
>>   Mark
>>   --
>>   gmx-users mailing listgmx-users@gromacs.org
>>
>>   >
>>
>>
>>   http://lists.gromacs.org/mailman/listinfo/gmx-users
>>   Please search the archive at
>>   http://www.gromacs.org/Support/Mailing_L

Re: [gmx-users] Inaccurate pressure readings

from -1000 to 1000, depending on the system.  The simulation box is 8x8x8 nm
(roughly) and contains about 12,000 atoms

On Thu, Jan 20, 2011 at 3:09 PM, Justin A. Lemkul  wrote:

>
>
> Denny Frost wrote:
>
>> I am running a variety of NPT simulations with polar, non-polar, and ionic
>> compounds.  Although my results for density agree well with experimental
>> values, the pressures I get from g_energy are off by 1 to 3 orders of
>> magnitude.  In the log file, the pressure fluctuates around a lot from -400
>> to 400 bar, which seems to be normal according to other posts on this list,
>> but the average (which is what g_energy gives me) is not 1.0 bar, as I
>> specified.  Does anyone know how to correct this problem?
>>
>>
> What is the average value you're getting?  How long are your simulations?
>
> -Justin
>
>
>  Pressure coupling parameters:
>> Pcoupl  =  berendsen
>> pcoupltype  =  isotropic
>> tau_p   =  1.0
>> ref_p   =  1.0
>> compressibility =  4.5e-5
>>
>>
> --
> 
>
> 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
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Re: [gmx-users] Inaccurate pressure readings

The average I calculate is not within -10 to 10, it is on the order of -1000
to 1000

On Thu, Jan 20, 2011 at 3:11 PM, Dallas Warren wrote:

> You have a variable that is fluctuating over a range of 800+ units (three
> orders of magnitude) and want the average to be 1.0?
>
>
>
> It is not a problem as such.  If you can get a large enough data set of
> pressure data, and it will have to be very large, then you might get it
> close to one.
>
>
>
> But as long the average you calculate is within may be an order of
> magnitude (-10 to 10) then there is nothing to get too worried about.
>
>
>
> Catch ya,
>
> Dr. Dallas Warren
>
> Medicinal Chemistry and Drug Action
>
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3010
> dallas.war...@monash.edu
>
> +61 3 9903 9304
> -
> When the only tool you own is a hammer, every problem begins to resemble a
> nail.
>
>
>
> *From:* gmx-users-boun...@gromacs.org [mailto:
> gmx-users-boun...@gromacs.org] *On Behalf Of *Denny Frost
> *Sent:* Friday, 21 January 2011 9:07 AM
> *To:* gmx-users@gromacs.org
> *Subject:* [gmx-users] Inaccurate pressure readings
>
>
>
> I am running a variety of NPT simulations with polar, non-polar, and ionic
> compounds.  Although my results for density agree well with experimental
> values, the pressures I get from g_energy are off by 1 to 3 orders of
> magnitude.  In the log file, the pressure fluctuates around a lot from -400
> to 400 bar, which seems to be normal according to other posts on this list,
> but the average (which is what g_energy gives me) is not 1.0 bar, as I
> specified.  Does anyone know how to correct this problem?
>
>
>
> Pressure coupling parameters:
>
> Pcoupl  =  berendsen
>
> pcoupltype  =  isotropic
>
> tau_p   =  1.0
>
> ref_p   =  1.0
>
> compressibility =  4.5e-5
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
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RE: [gmx-users] Inaccurate pressure readings

2011-01-20 Thread Dallas Warren

You have a variable that is fluctuating over a range of 800+ units
(three orders of magnitude) and want the average to be 1.0?

 

It is not a problem as such.  If you can get a large enough data set of
pressure data, and it will have to be very large, then you might get it
close to one.

 

But as long the average you calculate is within may be an order of
magnitude (-10 to 10) then there is nothing to get too worried about.

 

Catch ya,

Dr. Dallas Warren

Medicinal Chemistry and Drug Action

Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@monash.edu

+61 3 9903 9304
-
When the only tool you own is a hammer, every problem begins to resemble
a nail. 

 

From: gmx-users-boun...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org] On Behalf Of Denny Frost
Sent: Friday, 21 January 2011 9:07 AM
To: gmx-users@gromacs.org
Subject: [gmx-users] Inaccurate pressure readings

 

I am running a variety of NPT simulations with polar, non-polar, and
ionic compounds.  Although my results for density agree well with
experimental values, the pressures I get from g_energy are off by 1 to 3
orders of magnitude.  In the log file, the pressure fluctuates around a
lot from -400 to 400 bar, which seems to be normal according to other
posts on this list, but the average (which is what g_energy gives me) is
not 1.0 bar, as I specified.  Does anyone know how to correct this
problem?

 

Pressure coupling parameters:

Pcoupl  =  berendsen

pcoupltype  =  isotropic

tau_p   =  1.0

ref_p   =  1.0

compressibility =  4.5e-5

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Re: [gmx-users] Inaccurate pressure readings




Denny Frost wrote:
I am running a variety of NPT simulations with polar, non-polar, and 
ionic compounds.  Although my results for density agree well with 
experimental values, the pressures I get from g_energy are off by 1 to 3 
orders of magnitude.  In the log file, the pressure fluctuates around a 
lot from -400 to 400 bar, which seems to be normal according to other 
posts on this list, but the average (which is what g_energy gives me) is 
not 1.0 bar, as I specified.  Does anyone know how to correct this problem?




What is the average value you're getting?  How long are your simulations?

-Justin


Pressure coupling parameters:
Pcoupl  =  berendsen
pcoupltype  =  isotropic
tau_p   =  1.0
ref_p   =  1.0
compressibility =  4.5e-5



--


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] Inaccurate pressure readings

I am running a variety of NPT simulations with polar, non-polar, and ionic
compounds.  Although my results for density agree well with experimental
values, the pressures I get from g_energy are off by 1 to 3 orders of
magnitude.  In the log file, the pressure fluctuates around a lot from -400
to 400 bar, which seems to be normal according to other posts on this list,
but the average (which is what g_energy gives me) is not 1.0 bar, as I
specified.  Does anyone know how to correct this problem?

Pressure coupling parameters:
Pcoupl  =  berendsen
pcoupltype  =  isotropic
tau_p   =  1.0
ref_p   =  1.0
compressibility =  4.5e-5
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Re: [gmx-users] (no subject)




trevor brown wrote:

Dear users,
How can we fix the position of some atoms?
 


Use position restraints or freeze groups.

-Justin


best wishes
trevor
 



--


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)

2011-01-20 Thread trevor brown

Dear users,
How can we fix the position of some atoms?

best wishes
trevor
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[gmx-users] Box size and potential energy calculation

2011-01-20 Thread Christian Mötzing

Hi,

I currently read through the GMX manual 4.5.3. I have two questions:

1) Density is calculated by the density of the material and the box
volume. But I can't find a reference on how the box size is calculated.
Can you point me to some literature?

2) I wanted to look up the calculation of the potential energy. Do I
understand the calculation correctly:
- pairwise sum over all molecules
- for each pair Coulomb, Lennard-Jones and bonded terms are summed
aswell
- the calculation involves the position of the molecules (for example
Lennard-Jones)


Thanks

Christian

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Re: [gmx-users] How to create an rtp file for a lipid?




Dr. Ramón Garduño-Juárez wrote:

  Dear All:

I am trying to build a lipid bilayer made of DMPC 
(Dimyristoylphosphatidylcholine) surrounding a putative membrane 
channel. Everything goes well until I come across with the use of 
pdb2gmx and further on to the use of gromp, where I realized that I need 
to add some information about DMPC, information that is supposed to be 
in the rtp format.




Using an .rtp is an unnecessarily laborious (and indirect) way to add a lipid 
topology.  Simply #include an .itp file.  You haven't said what force field 
you're trying to use, but for Gromos force fields, you can use the topology from 
Tieleman:


http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies

There are probably topologies out there for CHARMM, as well, but I don't have 
the link handy.


I have no idea how to build such rtp file for DMPC. I have read and 
practiced with all tutorials about the construction of lipid bilayer 
with GROMACS. I have also read the relevant information about rtp files 
in the GROMACS Manual. However, I still cannot figure out how to do this.




The procedure you're looking for is nearly identical to the membrane protein 
topology.  The only difference is the lipid :)


I will appreciate very much any help provided. I am stuck and would like 
to learn how to create an rtp file from scratch, which I am sure I need 
to do more than once during this project...


Investing time in an .rtp file is probably not useful here, but if you're intent 
on doing it, simply read through the .rtp file for your force field and see how 
the existing building blocks are built.  If I were you, I would not waste my 
time doing so.


-Justin



Much obliged,
Ramon Garduno



--


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] How to create an rtp file for a lipid?

2011-01-20 Thread Dr. Ramón Garduño-Juárez


Dear All:

I am trying to build a lipid bilayer made of DMPC 
(Dimyristoylphosphatidylcholine) surrounding a putative membrane 
channel. Everything goes well until I come across with the use of 
pdb2gmx and further on to the use of gromp, where I realized that I need 
to add some information about DMPC, information that is supposed to be 
in the rtp format.


I have no idea how to build such rtp file for DMPC. I have read and 
practiced with all tutorials about the construction of lipid bilayer 
with GROMACS. I have also read the relevant information about rtp files 
in the GROMACS Manual. However, I still cannot figure out how to do this.


I will appreciate very much any help provided. I am stuck and would like 
to learn how to create an rtp file from scratch, which I am sure I need 
to do more than once during this project...


Much obliged,
Ramon Garduno
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Re: [gmx-users] How to install a new Forcefield in Gromacs 4.5.3

Qin Qiao wrote:

2011/1/20 Justin A. Lemkul mailto:jalem...@vt.edu>>

Qin Qiao wrote:

2011/1/20 Justin A. Lemkul mailto:jalem...@vt.edu> >>

   Qin Qiao wrote:

   Dear all,

   I would like to try a new forcefield in Gromacs 4.5.3. What
   should I do after I copied the ff to /share/gromacs/top
   directory? It seems the original FF.dat doesn't exist in
4.5.3..
   Could you give me some help?

   pdb2gmx detects forcefield directories by searching for names
that
   end in .ff, then looking in that directory for a "forcefield.doc"
   file that contains a brief description of the force field.

   -Justin

Thanks. But I cannot find the new forcefield when I used
pdb2gmx.. the folder of ff is named 'PACE.ff'

It must also contain a forcefield.itp file to be recognized, and
ultimately, to work at all.  I did a test of minimum requirements,
and only after I added a dummy forcefield.itp file to the test.ff
subdirectory did pdb2gmx recognize the new force field.

-Justin

There is an .itp file in the ff.. but it doesn't work.. strange.. is 
there any other possibility?

It works just fine for me.  To be sure, I used the name "PACE.ff" instead of my 
generic "test.ff" to make sure capitalization or something foolish wasn't a 
problem.  It worked fine, adding "PACE" as entry 16 in the pdb2gmx menu (I also 
have another custom force field, so the order of your pdb2gmx output may be 
different).

The other thing to try is to build the force field in your working directory and 
see if pdb2gmx finds it there.  This is, of course, not strictly required (and 
would be very inconvenient), but it could be a useful diagnostic.

-Justin

   Best,

   Qin

   -- 

   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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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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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 install a new Forcefield in Gromacs 4.5.3

2011/1/20 Justin A. Lemkul 

>
>
> Qin Qiao wrote:
>
>>
>>
>> 2011/1/20 Justin A. Lemkul mailto:jalem...@vt.edu>>
>>
>>
>>
>>
>>Qin Qiao wrote:
>>
>>Dear all,
>>
>>I would like to try a new forcefield in Gromacs 4.5.3. What
>>should I do after I copied the ff to /share/gromacs/top
>>directory? It seems the original FF.dat doesn't exist in 4.5.3..
>>Could you give me some help?
>>
>>
>>pdb2gmx detects forcefield directories by searching for names that
>>end in .ff, then looking in that directory for a "forcefield.doc"
>>file that contains a brief description of the force field.
>>
>>-Justin
>>
>>
>> Thanks. But I cannot find the new forcefield when I used pdb2gmx.. the
>> folder of ff is named 'PACE.ff'
>>
>
> It must also contain a forcefield.itp file to be recognized, and
> ultimately, to work at all.  I did a test of minimum requirements, and only
> after I added a dummy forcefield.itp file to the test.ff subdirectory did
> pdb2gmx recognize the new force field.
>
> -Justin
>
>
>> There is an .itp file in the ff.. but it doesn't work.. strange.. is there
any other possibility?

>
>>Best,
>>
>>Qin
>>
>>
>>-- 
>>
>>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
>>
>>
>>
> --
> 
>
> 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: Viewing results from Groamcs QM/MM sims

2011-01-20 Thread Sergio Manzetti

Hi everyone,


Does anyone have a suggestion for a free program to view QM/MM results from
Gromacs?

Thanks

"The HiJacker"

a.ka. S
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Re: [gmx-users] How to install a new Forcefield in Gromacs 4.5.3




Qin Qiao wrote:



2011/1/20 Justin A. Lemkul mailto:jalem...@vt.edu>>



Qin Qiao wrote:

Dear all,

I would like to try a new forcefield in Gromacs 4.5.3. What
should I do after I copied the ff to /share/gromacs/top
directory? It seems the original FF.dat doesn't exist in 4.5.3..
Could you give me some help?


pdb2gmx detects forcefield directories by searching for names that
end in .ff, then looking in that directory for a "forcefield.doc"
file that contains a brief description of the force field.

-Justin


Thanks. But I cannot find the new forcefield when I used pdb2gmx.. the 
folder of ff is named 'PACE.ff'


It must also contain a forcefield.itp file to be recognized, and ultimately, to 
work at all.  I did a test of minimum requirements, and only after I added a 
dummy forcefield.itp file to the test.ff subdirectory did pdb2gmx recognize the 
new force field.


-Justin




Best,

Qin


-- 



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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--


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 install a new Forcefield in Gromacs 4.5.3

2011/1/20 Justin A. Lemkul 

>
>
> Qin Qiao wrote:
>
>> Dear all,
>>
>> I would like to try a new forcefield in Gromacs 4.5.3. What should I do
>> after I copied the ff to /share/gromacs/top directory? It seems the original
>> FF.dat doesn't exist in 4.5.3.. Could you give me some help?
>>
>>
> pdb2gmx detects forcefield directories by searching for names that end in
> .ff, then looking in that directory for a "forcefield.doc" file that
> contains a brief description of the force field.
>
> -Justin
>

Thanks. But I cannot find the new forcefield when I used pdb2gmx.. the
folder of ff is named 'PACE.ff'

>
>  Best,
>>
>> Qin
>>
>>
> --
> 
>
> 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] avoiding bad contact in continutation run




Adwait Mevada wrote:

   1. Re: avoiding bad contact in continutation run (MarkAbraham)
Adwait Mevada wrote:



On 01/20/11, Adwait Mevada   wrote:


 Dear gmx-users,
 I am simulating a dppc + chol system, the force field is martini
with gromacs 3.3.3 the system was initially run for 150 ns, but i
had to later extend the simulation, so using the confout.gro and
with mdp options:
gen_vel = no
unconstrained_start = yes
 I gave a re-run for another 850 ns, now due to some interaction  the
box explodes after 460ns of run.I found that the cause was due  to
some unwanted bad contact.
It is important that the system continue from the previous state,
but the extension is leading to this bad contact.



Actually, you didn't preserve your ensemble if you used the .gro  file
for the coordinates. See
http://www.gromacs.org/Documentation/How-tos/Doing_Restarts Actually
 providing us with copies of the commands you're using is always a
good idea when asking for help.


150ns.gro was the output of the previous simulation run i.e. confout.gro
mdp file for the previous simulation is taken as is except for change of
simulation steps and making unconstrained_start = yes
grompp -np 8 -f 850ns.mdp -p dppc_chol.top -c 150ns.gro -o
512lip_256chol_850ns.tpr


As Mark suspected, you have failed to preserve your ensemble, due to 
the fact
that you're using a reduced precision (.gro) format for coordinates, 
 and you are
not supplying the .trr and .edr file from the previous run, so you're 
losing

velocities, temperature and pressure coupling information, etc.

-Justin

so i should be doing something like
tpbconv -s 512lip_150ns.tpr -f 512lip_150ns.trr -e 512lip_150ns.edr -o 
512lip_850ns.tpr -extend 850


mpiexe.openmpi -np 8 mdrun_mpi.openmpi -np 8 -s 512lip_850ns.tpr
 -o 512lip_850ns -e 512lip_850ns -g 512lip_850ns &



Yes, that would be an appropriate set of commands to extend the run.

-Justin


mpiexe.openmpi -np 8 mdrun_mpi.openmpi -np 8 -s 512lip_256chol_850ns.tpr
-o 512lip_256chol_850ns -e 512lip_256chol_850ns -g 
512lip_256chol_850ns &



Mark



My question is, is there a way to avoid this while retaining the
continuation of the previous simulation?
 Is using lower precision file a solution to this problem? if yes
how do i go about it.
-Adwait


This message was sent using IMP, the Internet Messaging Program.

--



-Adwait


This message was sent using IMP, the Internet Messaging Program.



--


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] Re: gmx-users Digest, Vol 81, Issue 140


   1. Re: avoiding bad contact in continutation run (Mark   Abraham)
Adwait Mevada wrote:



On 01/20/11, Adwait Mevada   wrote:


 Dear gmx-users,
 I am simulating a dppc + chol system, the force field is martini
with gromacs 3.3.3 the system was initially run for 150 ns, but i
had to later extend the simulation, so using the confout.gro and
with mdp options:
gen_vel = no
unconstrained_start = yes
 I gave a re-run for another 850 ns, now due to some interaction  the
box explodes after 460ns of run.I found that the cause was due  to
some unwanted bad contact.
It is important that the system continue from the previous state,
but the extension is leading to this bad contact.



Actually, you didn't preserve your ensemble if you used the .gro  file
for the coordinates. See
http://www.gromacs.org/Documentation/How-tos/Doing_Restarts Actually
 providing us with copies of the commands you're using is always a
good idea when asking for help.


150ns.gro was the output of the previous simulation run i.e. confout.gro
mdp file for the previous simulation is taken as is except for change of
simulation steps and making unconstrained_start = yes
grompp -np 8 -f 850ns.mdp -p dppc_chol.top -c 150ns.gro -o
512lip_256chol_850ns.tpr


As Mark suspected, you have failed to preserve your ensemble, due to the fact
that you're using a reduced precision (.gro) format for coordinates,  
 and you are

not supplying the .trr and .edr file from the previous run, so you're losing
velocities, temperature and pressure coupling information, etc.

-Justin

so i should be doing something like
tpbconv -s 512lip_150ns.tpr -f 512lip_150ns.trr -e 512lip_150ns.edr -o  
512lip_850ns.tpr -extend 850


mpiexe.openmpi -np 8 mdrun_mpi.openmpi -np 8 -s 512lip_850ns.tpr
 -o 512lip_850ns -e 512lip_850ns -g 512lip_850ns &


mpiexe.openmpi -np 8 mdrun_mpi.openmpi -np 8 -s 512lip_256chol_850ns.tpr
-o 512lip_256chol_850ns -e 512lip_256chol_850ns -g 512lip_256chol_850ns &


Mark



My question is, is there a way to avoid this while retaining the
continuation of the previous simulation?
 Is using lower precision file a solution to this problem? if yes
how do i go about it.
-Adwait


This message was sent using IMP, the Internet Messaging Program.

--



-Adwait


This message was sent using IMP, the Internet Messaging Program.

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Re: [gmx-users] How to install a new Forcefield in Gromacs 4.5.3




Qin Qiao wrote:

Dear all,

I would like to try a new forcefield in Gromacs 4.5.3. What should I do 
after I copied the ff to /share/gromacs/top directory? It seems the 
original FF.dat doesn't exist in 4.5.3.. Could you give me some help?




pdb2gmx detects forcefield directories by searching for names that end in .ff, 
then looking in that directory for a "forcefield.doc" file that contains a brief 
description of the force field.


-Justin


Best,

Qin



--


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] How to install a new Forcefield in Gromacs 4.5.3

Dear all,

I would like to try a new forcefield in Gromacs 4.5.3. What should I do
after I copied the ff to /share/gromacs/top directory? It seems the original
FF.dat doesn't exist in 4.5.3.. Could you give me some help?

Best,

Qin
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RE: [gmx-users] 4 x Opteron 12-core or 4 x Xeon 8-core ?

2011-01-20 Thread Berk Hess


Hi,

For systems or your size, they should run about equally fast.

Berk

> From: davidmcgiv...@gmail.com
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] 4 x Opteron 12-core or 4 x Xeon 8-core ? 
> Date: Thu, 20 Jan 2011 14:39:14 +0100
> 
> Dear Carsten,
> 
> Thanks for the advice!
> 
> The thing is that considering the price differences, we could buy 2-3  
> AMD machines (48 core) for each 1 Intel machine (32) core.
> 
> I'm only curious about how much faster Intel will be. Side to side,  
> amd 48core vs intel 32core, would make us talk about 2x differences in  
> ns/day?
> 
> Thanks again.
> 
> Regards,
> David
> 
> >
> > Message: 1
> > Date: Thu, 20 Jan 2011 13:45:54 +0100
> > From: Carsten Kutzner 
> > Subject: Re: [gmx-users] 4 x Opteron 12-core or 4 x Xeon 8-core ?
> > To: "Discussion list for GROMACS users" 
> > Message-ID: 
> > Content-Type: text/plain; charset=us-ascii
> >
> > Hi David,
> >
> > On Jan 20, 2011, at 1:21 PM, David McGiven wrote:
> >
> >> Dear Gromacs Users,
> >>
> >> We're going to buy a new server for HPC. It is going to run mainly  
> >> Gromacs calculations.
> >>
> >> Regarding Gromacs performance, I'm wondering which one, you Gromacs  
> >> users and developers, think will be faster.
> >>
> >> AMD Server :   4 x AMD Opteron 6176 12-core 2.3 Ghz + 96GB Memory  
> >> (2GB / core)
> >> Intel Server : 4 x Intel Xeon 8-core 2.66 Ghz + 64 GB RAM (2GB /  
> >> core)
> >>
> >> We normally run ~100k atom systems with PME and explicit water.
> >>
> >> Which one would you recommend ?
> >>
> >> Also, of course, AMD Server is cheaper. But we are mainly  
> >> interested on performance.
> >
> > If you have a fixed amount of money, you will get the most ns/day
> > if you buy the AMD Magny Cours machines. Each one will be slower  
> > compared to the
> > Intel server but you will get more servers altogether, thus more total
> > performance. If you can only buy a single server and you do not care  
> > about
> > what it costs, the Intel will be faster for shure.
> > Note that you do not need 2 GB/core for 100k atoms MD systems if you  
> > run
> > Gromacs. Half of it will be more than enough.
> >
> > Carsten
> >
> >
> >> Thanks.
> >>
> >> Best Regards,
> >> David
> >>
> >>
> >> -- 
> >> 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 thewww  
> >> interface or send it to gmx-users-requ...@gromacs.org.
> >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> >
> > --
> > Dr. Carsten Kutzner
> > Max Planck Institute for Biophysical Chemistry
> > Theoretical and Computational Biophysics
> > Am Fassberg 11, 37077 Goettingen, Germany
> > Tel. +49-551-2012313, Fax: +49-551-2012302
> > http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne
> >
> >
> 
> -- 
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Re: [gmx-users] 4 x Opteron 12-core or 4 x Xeon 8-core ?

2011-01-20 Thread David McGiven


Dear Carsten,

Thanks for the advice!

The thing is that considering the price differences, we could buy 2-3  
AMD machines (48 core) for each 1 Intel machine (32) core.


I'm only curious about how much faster Intel will be. Side to side,  
amd 48core vs intel 32core, would make us talk about 2x differences in  
ns/day?


Thanks again.

Regards,
David



Message: 1
Date: Thu, 20 Jan 2011 13:45:54 +0100
From: Carsten Kutzner 
Subject: Re: [gmx-users] 4 x Opteron 12-core or 4 x Xeon 8-core ?
To: "Discussion list for GROMACS users" 
Message-ID: 
Content-Type: text/plain; charset=us-ascii

Hi David,

On Jan 20, 2011, at 1:21 PM, David McGiven wrote:


Dear Gromacs Users,

We're going to buy a new server for HPC. It is going to run mainly  
Gromacs calculations.


Regarding Gromacs performance, I'm wondering which one, you Gromacs  
users and developers, think will be faster.


AMD Server :   4 x AMD Opteron 6176 12-core 2.3 Ghz + 96GB Memory  
(2GB / core)
Intel Server : 4 x Intel Xeon 8-core 2.66 Ghz + 64 GB RAM (2GB /  
core)


We normally run ~100k atom systems with PME and explicit water.

Which one would you recommend ?

Also, of course, AMD Server is cheaper. But we are mainly  
interested on performance.


If you have a fixed amount of money, you will get the most ns/day
if you buy the AMD Magny Cours machines. Each one will be slower  
compared to the

Intel server but you will get more servers altogether, thus more total
performance. If you can only buy a single server and you do not care  
about

what it costs, the Intel will be faster for shure.
Note that you do not need 2 GB/core for 100k atoms MD systems if you  
run

Gromacs. Half of it will be more than enough.

Carsten



Thanks.

Best Regards,
David


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 before posting!
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--
Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302
http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne




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[gmx-users] different versions- different output!

2011-01-20 Thread jojo J

Hello all,

I am a little confused since I am not getting the same output from the same
input files using two different versions (the most recent one: 4.5.3 and
4.0.7). I am using two different machines and size of data generated from
these simulations are not the same either. Below is the output of grommp on
4.5.3 which results in segmentaion fault error. The other version gives no
error and I get trr file without any problem. System is stable and it is
equilibrated.. Can you please help me and guide me how to deal with the
following errors and why is this happening?

many many thanks,


NOTE 1 [file md-.mdp]:
  nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
  nstcomm to nstcalcenergy

Generated 332520 of the 332520 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 332520 of the 332520 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'Polymer'
Velocities were taken from a Maxwell distribution at 300 K
Number of degrees of freedom in T-Coupling group System is 8685.00

NOTE 2 [file md.mdp]:
  The sum of the two largest charge group radii (0.204120) is larger than
  rlist (1.10) - rvdw (1.00)

This run will generate roughly 35 Mb of data
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Re: [gmx-users] Re: Problem in Disulfide Bond

2011-01-20 Thread Oliver Grant

In the pdb, before pdb2gmx, rename the CYS residues involved in the S-S
bonds as CYS2.
If you don't know this then you need to read everything on this page about
using the amberports:
http://ffamber.cnsm.csulb.edu/
As you may have other issues with HIS and LYS residues.

Oliver
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[gmx-users] QM/MM viewer

2011-01-20 Thread Sergio Manzetti

Does anyone know of a free-of-charge viewer for QM/MM results from G03, for
Ubuntu? It should be able to show electron orbitals, polarizabilities, bond
strength etc.

Sergio
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Re: [gmx-users] Re: avoiding bad contact in continutation run (Mark Abraham)

Adwait Mevada wrote:

On 01/20/11, Adwait Mevada wrote:

Dear gmx-users,
I am simulating a dppc + chol system, the force field is martini
with gromacs 3.3.3 the system was initially run for 150 ns, but i
had to later extend the simulation, so using the confout.gro and
with mdp options:

gen_vel = no
unconstrained_start = yes
I gave a re-run for another 850 ns, now due to some interaction the
box explodes after 460ns of run.I found that the cause was due to
some unwanted bad contact.
It is important that the system continue from the previous state,
but the extension is leading to this bad contact.

Actually, you didn't preserve your ensemble if you used the .gro file
for the coordinates. See
http://www.gromacs.org/Documentation/How-tos/Doing_Restarts Actually
providing us with copies of the commands you're using is always a
good idea when asking for help.

As Mark suspected, you have failed to preserve your ensemble, due to the fact
that you're using a reduced precision (.gro) format for coordinates, and you are
not supplying the .trr and .edr file from the previous run, so you're losing
velocities, temperature and pressure coupling information, etc.

-Justin

mpiexe.openmpi -np 8 mdrun_mpi.openmpi -np 8 -s 512lip_256chol_850ns.tpr
-o 512lip_256chol_850ns -e 512lip_256chol_850ns -g 512lip_256chol_850ns &

Mark

My question is, is there a way to avoid this while retaining the
continuation of the previous simulation?
Is using lower precision file a solution to this problem? if yes
how do i go about it.

-Adwait

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-Adwait

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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] QM/MM viewer (was: CNT)



As much as I appreciate being seen as a reliable source of information, I have 
no experience with this program and no time to investigate it on my own.  Please 
remember a few things:


First, please do not hijack someone else's thread to ask an unrelated question.

Second, this is a forum for Gromacs support, not private requests to have people 
figure out how to install stuff for you.


Third, complete installation instructions are given on the site you link.  I 
suspect you should be able to follow those instructions.


-Justin

Sergio Manzetti wrote:
Dear Justin, I got the impression that you know a lot on Linux, and was 
wondering if you are able to see how this package can be successfully 
installed on Ubuntu? Its for viewing QM/MM results. I find it quite 
interesting as a package, and it has a lot of nice graphics. If you 
should be able to check this out, do you know of a free QM/MM viewer 
which is able to open electron density maps, show polarizabilities and 
bond strentgth and such?

I am using Gaussian 03 as a generator of QM/MM data.

http://www.scl.ameslab.gov/~brett/MacMolPlt/linux-support.shtml

Thanks and best wishes

Sergio


--


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] Re: avoiding bad contact in continutation run (Mark Abraham)

On 01/20/11, Adwait Mevada wrote:

gen_vel = no
unconstrained_start = yes
I gave a re-run for another 850 ns, now due to some interaction
the box explodes after 460ns of run.I found that the cause was due
to some unwanted bad contact.
It is important that the system continue from the previous state,
but the extension is leading to this bad contact.

Actually, you didn't preserve your ensemble if you used the .gro
file for the coordinates. See
http://www.gromacs.org/Documentation/How-tos/Doing_Restarts Actually
providing us with copies of the commands you're using is always a
good idea when asking for help.

150ns.gro was the output of the previous simulation run i.e. confout.gro
mdp file for the previous simulation is taken as is except for change of
simulation steps and making unconstrained_start = yes
grompp -np 8 -f 850ns.mdp -p dppc_chol.top -c 150ns.gro -o
512lip_256chol_850ns.tpr
mpiexe.openmpi -np 8 mdrun_mpi.openmpi -np 8 -s
512lip_256chol_850ns.tpr -o 512lip_256chol_850ns -e
512lip_256chol_850ns -g 512lip_256chol_850ns &

Mark

My question is, is there a way to avoid this while retaining the
continuation of the previous simulation?
Is using lower precision file a solution to this problem? if yes
how do i go about it.

-Adwait

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Re: [gmx-users] non-integer charge in a protein setup using pdb2gmx AND slow simulations in vacuum v. 4.5.3

maria goranovic wrote:
I did use -ter and chose -COO and NH3+. Am i supposed to chose 
Zwitterion_COO- and Zwitterion_NH3+ ? 

That's what I said, and that's what you have, isn't it?  A single amino acid 
that should have both its termini charged?

-Justin

On Thu, Jan 20, 2011 at 12:55 PM, Justin A. Lemkul > wrote:

maria goranovic wrote:

Hi

I have figured out the vacuum slow problem. It turns out I was
using PBC in vacuum with PME. It is now fixed.

The other problem is still there. My protein has 2 chains. one
chain is simply a glutamate residue. Its charge (both terminii
charged is -1.11 instead of -1). here is the section of the
topology with the charges. Why does pdb2gmx assign a charge of
-1.11 instead of -1 if there is a free glutamate molecule with
NH3+ and COO- at the terminii ?

You're not choosing the termini correctly.  Use -ter with pdb2gmx
and select the zwitterion forms of both termini.

-Justin

1   opls_287484GLU  N  1   -0.3  
 14.0067   ; qtot -0.3
2   opls_290484GLU H1  1   0.33
 1.008   ; qtot 0.03
3   opls_290484GLU H2  1   0.33
 1.008   ; qtot 0.36
4   opls_290484GLU H3  1   0.33
 1.008   ; qtot 0.69
5   opls_283484GLU CA  1   0.04
12.011   ; qtot 0.73
6   opls_140484GLU HA  1   0.06
 1.008   ; qtot 0.79
7   opls_136484GLU CB  2  -0.12
12.011   ; qtot 0.67
8   opls_140484GLUHB1  2   0.06
 1.008   ; qtot 0.73
9   opls_140484GLUHB2  2   0.06
 1.008   ; qtot 0.79
   10   opls_274484GLU CG  3  -0.22
12.011   ; qtot 0.57
   11   opls_140484GLUHG1  3   0.06
 1.008   ; qtot 0.63
   12   opls_140484GLUHG2  3   0.06
 1.008   ; qtot 0.69
   13   opls_271484GLU CD  40.7
12.011   ; qtot 1.39
   14   opls_272484GLUOE1  4   -0.8  
 15.9994   ; qtot 0.59
   15   opls_272484GLUOE2  4   -0.8  
 15.9994   ; qtot -0.21
   16   opls_271484GLU  C  50.7
12.011   ; qtot 0.49
   17   opls_272484GLU O1  5   -0.8  
 15.9994   ; qtot -0.31
   18   opls_272484GLU O2  5   -0.8  
 15.9994   ; qtot -1.11

On Thu, Jan 20, 2011 at 11:55 AM, Mark Abraham
mailto:mark.abra...@anu.edu.au>
>> wrote:

   On 01/20/11, *maria goranovic * mailto:mariagorano...@gmail.com>
   >> wrote:

   Hi

   I have a protein whose topology I built using pdb2gmx
with the -ss
   option and the opls-aa force field. When I run grompp,
the total
   charge on the protein is reported as 2.9 (not 2.999). Why a
   non-zero charge? Does this have something to do with the
disulfide
   bridge?

   Something is materially wrong, like mangled termini. Have a
look at
   the resulting structure.

   Secondly, when I run a simulation of the same protein
(7000 atoms)
   with certain restraints in vacuum, the simulation runs
very slow.
   I am wondering why. I am not using particle
decomposition. the box
   size is 50 x 50 x 50 nm. Using 4.5.3

   Have a look at the end of the .log file for some performance
data.
   How are you assessing "very slow"?

   Mark
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Copenhag

Re: [gmx-users] non-integer charge in a protein setup using pdb2gmx AND slow simulations in vacuum v. 4.5.3

I did use -ter and chose -COO and NH3+. Am i supposed to chose
Zwitterion_COO- and Zwitterion_NH3+ ?

On Thu, Jan 20, 2011 at 12:55 PM, Justin A. Lemkul  wrote:

>
>
> maria goranovic wrote:
>
>> Hi
>>
>> I have figured out the vacuum slow problem. It turns out I was using PBC
>> in vacuum with PME. It is now fixed.
>>
>> The other problem is still there. My protein has 2 chains. one chain is
>> simply a glutamate residue. Its charge (both terminii charged is -1.11
>> instead of -1). here is the section of the topology with the charges. Why
>> does pdb2gmx assign a charge of -1.11 instead of -1 if there is a free
>> glutamate molecule with NH3+ and COO- at the terminii ?
>>
>
> You're not choosing the termini correctly.  Use -ter with pdb2gmx and
> select the zwitterion forms of both termini.
>
> -Justin
>
>
>> 1   opls_287484GLU  N  1   -0.314.0067   ;
>> qtot -0.3
>> 2   opls_290484GLU H1  1   0.33  1.008   ;
>> qtot 0.03
>> 3   opls_290484GLU H2  1   0.33  1.008   ;
>> qtot 0.36
>> 4   opls_290484GLU H3  1   0.33  1.008   ;
>> qtot 0.69
>> 5   opls_283484GLU CA  1   0.04 12.011   ;
>> qtot 0.73
>> 6   opls_140484GLU HA  1   0.06  1.008   ;
>> qtot 0.79
>> 7   opls_136484GLU CB  2  -0.12 12.011   ;
>> qtot 0.67
>> 8   opls_140484GLUHB1  2   0.06  1.008   ;
>> qtot 0.73
>> 9   opls_140484GLUHB2  2   0.06  1.008   ;
>> qtot 0.79
>>10   opls_274484GLU CG  3  -0.22 12.011   ;
>> qtot 0.57
>>11   opls_140484GLUHG1  3   0.06  1.008   ;
>> qtot 0.63
>>12   opls_140484GLUHG2  3   0.06  1.008   ;
>> qtot 0.69
>>13   opls_271484GLU CD  40.7 12.011   ;
>> qtot 1.39
>>14   opls_272484GLUOE1  4   -0.815.9994   ;
>> qtot 0.59
>>15   opls_272484GLUOE2  4   -0.815.9994   ;
>> qtot -0.21
>>16   opls_271484GLU  C  50.7 12.011   ;
>> qtot 0.49
>>17   opls_272484GLU O1  5   -0.815.9994   ;
>> qtot -0.31
>>18   opls_272484GLU O2  5   -0.815.9994   ;
>> qtot -1.11
>>
>>
>>
>> On Thu, Jan 20, 2011 at 11:55 AM, Mark Abraham 
>> > mark.abra...@anu.edu.au>> wrote:
>>
>>
>>
>>On 01/20/11, *maria goranovic * >> wrote:
>>
>>>Hi
>>>
>>>I have a protein whose topology I built using pdb2gmx with the -ss
>>>option and the opls-aa force field. When I run grompp, the total
>>>charge on the protein is reported as 2.9 (not 2.999). Why a
>>>non-zero charge? Does this have something to do with the disulfide
>>>bridge?
>>>
>>
>>Something is materially wrong, like mangled termini. Have a look at
>>the resulting structure.
>>
>>
>> Secondly, when I run a simulation of the same protein (7000 atoms)
>>>with certain restraints in vacuum, the simulation runs very slow.
>>>I am wondering why. I am not using particle decomposition. the box
>>>size is 50 x 50 x 50 nm. Using 4.5.3
>>>
>>
>>Have a look at the end of the .log file for some performance data.
>>How are you assessing "very slow"?
>>
>>Mark
>>--
>>gmx-users mailing listgmx-users@gromacs.org
>>
>>
>>http://lists.gromacs.org/mailman/listinfo/gmx-users
>>Please search the archive at
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>>
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>>
>>
>>
>> --
>> Maria G.
>> Technical University of Denmark
>> Copenhagen
>>
>>
> --
> 
>
> 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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Technical University of Denmark
Copenhagen
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Re: [gmx-users] 4 x Opteron 12-core or 4 x Xeon 8-core ?

2011-01-20 Thread Carsten Kutzner

Hi David,

On Jan 20, 2011, at 1:21 PM, David McGiven wrote:

> Dear Gromacs Users,
> 
> We're going to buy a new server for HPC. It is going to run mainly Gromacs 
> calculations.
> 
> Regarding Gromacs performance, I'm wondering which one, you Gromacs users and 
> developers, think will be faster.
> 
> AMD Server :   4 x AMD Opteron 6176 12-core 2.3 Ghz + 96GB Memory (2GB / core)
> Intel Server : 4 x Intel Xeon 8-core 2.66 Ghz + 64 GB RAM (2GB / core)
> 
> We normally run ~100k atom systems with PME and explicit water.
> 
> Which one would you recommend ?
> 
> Also, of course, AMD Server is cheaper. But we are mainly interested on 
> performance.

If you have a fixed amount of money, you will get the most ns/day 
if you buy the AMD Magny Cours machines. Each one will be slower compared to the
Intel server but you will get more servers altogether, thus more total
performance. If you can only buy a single server and you do not care about
what it costs, the Intel will be faster for shure.
Note that you do not need 2 GB/core for 100k atoms MD systems if you run
Gromacs. Half of it will be more than enough.

Carsten


> Thanks.
> 
> Best Regards,
> David
> 
> 
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--
Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302
http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne




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Re: [gmx-users] avoiding bad contact in continutation run



On 01/20/11, Adwait Mevada   wrote:
> 
>  Dear gmx-users,
>  I am simulating a dppc + chol system, the force field is martini with 
> gromacs 3.3.3 the system was initially run for 150 ns, but i had to later 
> extend the simulation, so using the confout.gro and with mdp options:
> gen_vel = no
> unconstrained_start = yes
>  I gave a re-run for another 850 ns, now due to some interaction the box 
> explodes after 460ns of run.I found that the cause was due to some unwanted 
> bad contact.
> It is important that the system continue from the previous state, but the 
> extension is leading to this bad contact.
> 

Actually, you didn't preserve your ensemble if you used the .gro file for the 
coordinates. See http://www.gromacs.org/Documentation/How-tos/Doing_Restarts 
Actually providing us with copies of the commands you're using is always a good 
idea when asking for help.

Mark

> 
> My question is, is there a way to avoid this while retaining the continuation 
> of the previous simulation?
>  Is using lower precision file a solution to this problem? if yes how do i go 
> about it.
> -Adwait
> 
> 
> This message was sent using IMP, the Internet Messaging Program.
> 
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[gmx-users] 4 x Opteron 12-core or 4 x Xeon 8-core ?

2011-01-20 Thread David McGiven


Dear Gromacs Users,

We're going to buy a new server for HPC. It is going to run mainly  
Gromacs calculations.


Regarding Gromacs performance, I'm wondering which one, you Gromacs  
users and developers, think will be faster.


AMD Server :   4 x AMD Opteron 6176 12-core 2.3 Ghz + 96GB Memory  
(2GB / core)

Intel Server : 4 x Intel Xeon 8-core 2.66 Ghz + 64 GB RAM (2GB / core)

We normally run ~100k atom systems with PME and explicit water.

Which one would you recommend ?

Also, of course, AMD Server is cheaper. But we are mainly interested  
on performance.


Thanks.

Best Regards,
David


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Re: [gmx-users] Re: Problem in Disulfide Bond



On 01/20/11, parthi...@ncbs.res.in wrote:
> > Message: 3
> > Date: Thu, 20 Jan 2011 09:30:00 +
> > From: Oliver Grant 
> > Subject: Re: [gmx-users] Re: Problem in Disulfide Bond
> > To: Discussion list for GROMACS users 
> > Message-ID:
> > 
> > Content-Type: text/plain; charset="iso-8859-1"
> >
> > Show us that part of your topology. When you used ffamberports have you
> > renamed the CYS to CYS2?
> >
> > Oliver
> >
> 
> could you explain this in detail where this change have to done.? i can
> check again.
> 
> > --
> >
> > Message: 4
> > Date: Thu, 20 Jan 2011 20:54:39 +1100
> > From: Mark Abraham 
> > Subject: Re: [gmx-users] Re: Problem in Disulfide Bond
> > To: Discussion list for GROMACS users 
> > Message-ID: <7690be842aff.4d38a...@anu.edu.au>
> > Content-Type: text/plain; charset="iso-8859-1"
> >
> >
> >
> >> > parthi...@ncbs.res.in wrote:
> >> >> Hi
> >> >>
> >> >> I am using a dimer for my simulation system which is connected by 2
> >> >> disulfide bonds.
> >> >> After energy minimization for even few cycles, the disulfide bond
> >> breaks
> >> >> which is not expected.
> >> >
> >> > Bonds do not break in classical molecular mechanics.  One of two
> >> things is
> >> > happening:
> >> >
> >> > 1. There was never a bond to begin with (check your topology)
> >> There do a bond exists.
> >>
> >
> > So you can see in your [bonds] section an entry for the two atom numbers?
> 
> I cant see any corresponding entry with res.to CYS residues.
> 

So you didn't make a bond. Anything you saw in pymol or vmd is irrelevant. They 
didn't read your .top file and that's what counts. You need to call pdb2gmx 
properly.

Mark

> >
> >
> >>
> >> > 2. The bond is highly strained, in which case something is wrong with
> >> your
> >> > structure.
> >> >
> >> >> i have applied amber99 force field and prepared the system. while i
> >> >> tried
> >> >> with another force field in Gromacs which did not worked at all.
> >> >
> >> > What does that mean?  What failed?
> >> As said previously the bond is strained only after pdb2gmx itself. is
> >> there any other way to fix it.
> >>
> >
> > Previously you said the bond was strained after EM. pdb2gmx is not capable
> > of straining a bond.
> >
> > Be sure you are not looking at "bonds" generated via heuristics in some
> > visualization program. If pdb2gmx is generating a disulfide bond, it will
> > say so in the standard output, and you will be able to find it in the
> > [bonds] section. Otherwise, there is no bond.
> >
> > Mark
> >
> 
> I used pymol and vmd to visualize this
> 
> Thanks
> Parthiban.
> 
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Re: [gmx-users] Re: Problem in Disulfide Bond

parthi...@ncbs.res.in wrote:

Message: 3
Date: Thu, 20 Jan 2011 09:30:00 +
From: Oliver Grant 
Subject: Re: [gmx-users] Re: Problem in Disulfide Bond
To: Discussion list for GROMACS users 
Message-ID:

Content-Type: text/plain; charset="iso-8859-1"

Show us that part of your topology. When you used ffamberports have you
renamed the CYS to CYS2?

Oliver

could you explain this in detail where this change have to done.? i can
check again.

If the disulfide was created by pdb2gmx, then specbond.dat will have done this 
for you and assigned the proper parameters.  Did pdb2gmx automatically assign 
your bond for you, or did you make post-pdb2gmx manual changes to your topology?

-Justin

--

Message: 4
Date: Thu, 20 Jan 2011 20:54:39 +1100
From: Mark Abraham 
Subject: Re: [gmx-users] Re: Problem in Disulfide Bond
To: Discussion list for GROMACS users 
Message-ID: <7690be842aff.4d38a...@anu.edu.au>
Content-Type: text/plain; charset="iso-8859-1"

parthi...@ncbs.res.in wrote:

Hi

I am using a dimer for my simulation system which is connected by 2
disulfide bonds.
After energy minimization for even few cycles, the disulfide bond

breaks

which is not expected.

Bonds do not break in classical molecular mechanics.  One of two

things is

happening:

1. There was never a bond to begin with (check your topology)

There do a bond exists.

So you can see in your [bonds] section an entry for the two atom numbers?

I cant see any corresponding entry with res.to CYS residues.

2. The bond is highly strained, in which case something is wrong with

your

structure.

i have applied amber99 force field and prepared the system. while i
tried
with another force field in Gromacs which did not worked at all.

What does that mean?  What failed?

As said previously the bond is strained only after pdb2gmx itself. is
there any other way to fix it.

Previously you said the bond was strained after EM. pdb2gmx is not capable
of straining a bond.

Be sure you are not looking at "bonds" generated via heuristics in some
visualization program. If pdb2gmx is generating a disulfide bond, it will
say so in the standard output, and you will be able to find it in the
[bonds] section. Otherwise, there is no bond.

Mark

I used pymol and vmd to visualize this

Thanks
Parthiban.

--

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] Re: Problem in Disulfide Bond

2011-01-20 Thread parthiban

> Message: 3
> Date: Thu, 20 Jan 2011 09:30:00 +
> From: Oliver Grant 
> Subject: Re: [gmx-users] Re: Problem in Disulfide Bond
> To: Discussion list for GROMACS users 
> Message-ID:
>   
> Content-Type: text/plain; charset="iso-8859-1"
>
> Show us that part of your topology. When you used ffamberports have you
> renamed the CYS to CYS2?
>
> Oliver
>

could you explain this in detail where this change have to done.? i can
check again.

> --
>
> Message: 4
> Date: Thu, 20 Jan 2011 20:54:39 +1100
> From: Mark Abraham 
> Subject: Re: [gmx-users] Re: Problem in Disulfide Bond
> To: Discussion list for GROMACS users 
> Message-ID: <7690be842aff.4d38a...@anu.edu.au>
> Content-Type: text/plain; charset="iso-8859-1"
>
>
>
>> > parthi...@ncbs.res.in wrote:
>> >> Hi
>> >>
>> >> I am using a dimer for my simulation system which is connected by 2
>> >> disulfide bonds.
>> >> After energy minimization for even few cycles, the disulfide bond
>> breaks
>> >> which is not expected.
>> >
>> > Bonds do not break in classical molecular mechanics.  One of two
>> things is
>> > happening:
>> >
>> > 1. There was never a bond to begin with (check your topology)
>> There do a bond exists.
>>
>
> So you can see in your [bonds] section an entry for the two atom numbers?

I cant see any corresponding entry with res.to CYS residues.

>
>
>>
>> > 2. The bond is highly strained, in which case something is wrong with
>> your
>> > structure.
>> >
>> >> i have applied amber99 force field and prepared the system. while i
>> >> tried
>> >> with another force field in Gromacs which did not worked at all.
>> >
>> > What does that mean?  What failed?
>> As said previously the bond is strained only after pdb2gmx itself. is
>> there any other way to fix it.
>>
>
> Previously you said the bond was strained after EM. pdb2gmx is not capable
> of straining a bond.
>
> Be sure you are not looking at "bonds" generated via heuristics in some
> visualization program. If pdb2gmx is generating a disulfide bond, it will
> say so in the standard output, and you will be able to find it in the
> [bonds] section. Otherwise, there is no bond.
>
> Mark
>

I used pymol and vmd to visualize this

Thanks
Parthiban.

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[gmx-users] avoiding bad contact in continutation run



 Dear gmx-users,
 I am simulating a dppc + chol system, the force field is martini  
with gromacs 3.3.3 the system was initially run for 150 ns, but i had  
to later extend the simulation, so using the confout.gro and with mdp  
options:

gen_vel = no
unconstrained_start = yes
 I gave a re-run for another 850 ns, now due to some interaction the  
box explodes after 460ns of run.I found that the cause was due to some  
unwanted bad contact.
It is important that the system continue from the previous state, but  
the extension is leading to this bad contact.
My question is, is there a way to avoid this while retaining the  
continuation of the previous simulation?
 Is using lower precision file a solution to this problem? if yes how  
do i go about it.

-Adwait


This message was sent using IMP, the Internet Messaging Program.

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Re: [gmx-users] non-integer charge in a protein setup using pdb2gmx AND slow simulations in vacuum v. 4.5.3




maria goranovic wrote:

Hi

I have figured out the vacuum slow problem. It turns out I was using PBC 
in vacuum with PME. It is now fixed.


The other problem is still there. My protein has 2 chains. one chain is 
simply a glutamate residue. Its charge (both terminii charged is -1.11 
instead of -1). here is the section of the topology with the charges. 
Why does pdb2gmx assign a charge of -1.11 instead of -1 if there is a 
free glutamate molecule with NH3+ and COO- at the terminii ? 



You're not choosing the termini correctly.  Use -ter with pdb2gmx and select the 
zwitterion forms of both termini.


-Justin



 1   opls_287484GLU  N  1   -0.314.0067   ; 
qtot -0.3
 2   opls_290484GLU H1  1   0.33  1.008   ; 
qtot 0.03
 3   opls_290484GLU H2  1   0.33  1.008   ; 
qtot 0.36
 4   opls_290484GLU H3  1   0.33  1.008   ; 
qtot 0.69
 5   opls_283484GLU CA  1   0.04 12.011   ; 
qtot 0.73
 6   opls_140484GLU HA  1   0.06  1.008   ; 
qtot 0.79
 7   opls_136484GLU CB  2  -0.12 12.011   ; 
qtot 0.67
 8   opls_140484GLUHB1  2   0.06  1.008   ; 
qtot 0.73
 9   opls_140484GLUHB2  2   0.06  1.008   ; 
qtot 0.79
10   opls_274484GLU CG  3  -0.22 12.011   ; 
qtot 0.57
11   opls_140484GLUHG1  3   0.06  1.008   ; 
qtot 0.63
12   opls_140484GLUHG2  3   0.06  1.008   ; 
qtot 0.69
13   opls_271484GLU CD  40.7 12.011   ; 
qtot 1.39
14   opls_272484GLUOE1  4   -0.815.9994   ; 
qtot 0.59
15   opls_272484GLUOE2  4   -0.815.9994   ; 
qtot -0.21
16   opls_271484GLU  C  50.7 12.011   ; 
qtot 0.49
17   opls_272484GLU O1  5   -0.815.9994   ; 
qtot -0.31
18   opls_272484GLU O2  5   -0.815.9994   ; 
qtot -1.11




On Thu, Jan 20, 2011 at 11:55 AM, Mark Abraham > wrote:




On 01/20/11, *maria goranovic * mailto:mariagorano...@gmail.com>> wrote:

Hi

I have a protein whose topology I built using pdb2gmx with the -ss
option and the opls-aa force field. When I run grompp, the total
charge on the protein is reported as 2.9 (not 2.999). Why a
non-zero charge? Does this have something to do with the disulfide
bridge?


Something is materially wrong, like mangled termini. Have a look at
the resulting structure.



Secondly, when I run a simulation of the same protein (7000 atoms)
with certain restraints in vacuum, the simulation runs very slow.
I am wondering why. I am not using particle decomposition. the box
size is 50 x 50 x 50 nm. Using 4.5.3


Have a look at the end of the .log file for some performance data.
How are you assessing "very slow"?

Mark
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--
Maria G.
Technical University of Denmark
Copenhagen



--


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] Mesa GLproto stuff UBUNTU

2011-01-20 Thread Sergio Manzetti

Hello, I am wondering if anyone has had luck installing glproto for a
functional Mesa package on Ubuntu? Thing is I am trying to install
wxmacmolplt-7.4.2 to view QM/MM results, but get nowhere without a
functional Open GL emulator.

Thanks

Sergio
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Re: [gmx-users] non-integer charge in a protein setup using pdb2gmx AND slow simulations in vacuum v. 4.5.3

Hi

I have figured out the vacuum slow problem. It turns out I was using PBC in
vacuum with PME. It is now fixed.

The other problem is still there. My protein has 2 chains. one chain is
simply a glutamate residue. Its charge (both terminii charged is -1.11
instead of -1). here is the section of the topology with the charges. Why
does pdb2gmx assign a charge of -1.11 instead of -1 if there is a free
glutamate molecule with NH3+ and COO- at the terminii ?


 1   opls_287484GLU  N  1   -0.314.0067   ; qtot
-0.3
 2   opls_290484GLU H1  1   0.33  1.008   ; qtot
0.03
 3   opls_290484GLU H2  1   0.33  1.008   ; qtot
0.36
 4   opls_290484GLU H3  1   0.33  1.008   ; qtot
0.69
 5   opls_283484GLU CA  1   0.04 12.011   ; qtot
0.73
 6   opls_140484GLU HA  1   0.06  1.008   ; qtot
0.79
 7   opls_136484GLU CB  2  -0.12 12.011   ; qtot
0.67
 8   opls_140484GLUHB1  2   0.06  1.008   ; qtot
0.73
 9   opls_140484GLUHB2  2   0.06  1.008   ; qtot
0.79
10   opls_274484GLU CG  3  -0.22 12.011   ; qtot
0.57
11   opls_140484GLUHG1  3   0.06  1.008   ; qtot
0.63
12   opls_140484GLUHG2  3   0.06  1.008   ; qtot
0.69
13   opls_271484GLU CD  40.7 12.011   ; qtot
1.39
14   opls_272484GLUOE1  4   -0.815.9994   ; qtot
0.59
15   opls_272484GLUOE2  4   -0.815.9994   ; qtot
-0.21
16   opls_271484GLU  C  50.7 12.011   ; qtot
0.49
17   opls_272484GLU O1  5   -0.815.9994   ; qtot
-0.31
18   opls_272484GLU O2  5   -0.815.9994   ; qtot
-1.11



On Thu, Jan 20, 2011 at 11:55 AM, Mark Abraham wrote:

>
>
> On 01/20/11, *maria goranovic *  wrote:
>
> Hi
>
> I have a protein whose topology I built using pdb2gmx with the -ss option
> and the opls-aa force field. When I run grompp, the total charge on the
> protein is reported as 2.9 (not 2.999). Why a non-zero charge? Does this
> have something to do with the disulfide bridge?
>
>
> Something is materially wrong, like mangled termini. Have a look at the
> resulting structure.
>
>
> Secondly, when I run a simulation of the same protein (7000 atoms) with
> certain restraints in vacuum, the simulation runs very slow. I am wondering
> why. I am not using particle decomposition. the box size is 50 x 50 x 50 nm.
> Using 4.5.3
>
>
> Have a look at the end of the .log file for some performance data. How are
> you assessing "very slow"?
>
> Mark
> --
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-- 
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Technical University of Denmark
Copenhagen
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Re: [gmx-users] non-integer charge in a protein setup using pdb2gmx AND slow simulations in vacuum v. 4.5.3



On 01/20/11, maria goranovic   wrote:
> Hi
> 
> I have a protein whose topology I built using pdb2gmx with the -ss option and 
> the opls-aa force field. When I run grompp, the total charge on the protein 
> is reported as 2.9 (not 2.999). Why a non-zero charge? Does this have 
> something to do with the disulfide bridge?
> 
> 

Something is materially wrong, like mangled termini. Have a look at the 
resulting structure.


> Secondly, when I run a simulation of the same protein (7000 atoms) with 
> certain restraints in vacuum, the simulation runs very slow. I am wondering 
> why. I am not using particle decomposition. the box size is 50 x 50 x 50 nm. 
> Using 4.5.3
> 
> 

Have a look at the end of the .log file for some performance data. How are you 
assessing "very slow"?

Mark
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[gmx-users] non-integer charge in a protein setup using pdb2gmx AND slow simulations in vacuum v. 4.5.3

Hi

I have a protein whose topology I built using pdb2gmx with the -ss option
and the opls-aa force field. When I run grompp, the total charge on the
protein is reported as 2.9 (not 2.999). Why a non-zero charge? Does this
have something to do with the disulfide bridge?

Secondly, when I run a simulation of the same protein (7000 atoms) with
certain restraints in vacuum, the simulation runs very slow. I am wondering
why. I am not using particle decomposition. the box size is 50 x 50 x 50 nm.
Using 4.5.3

-- 
Maria G.
Technical University of Denmark
Copenhagen
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Re: [gmx-users] Re: Problem in Disulfide Bond



On 01/20/11, parthi...@ncbs.res.in wrote:
> > Message: 5
> > Date: Wed, 19 Jan 2011 08:37:20 -0500
> > From: "Justin A. Lemkul" 
> > Subject: Re: [gmx-users] Re: Problem in Disulfide Bond
> > To: Discussion list for GROMACS users 
> > Message-ID: <4d36e910.6030...@vt.edu>
> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> >
> >
> >
> > parthi...@ncbs.res.in wrote:
> >> Hi
> >>
> >> I am using a dimer for my simulation system which is connected by 2
> >> disulfide bonds.
> >> After energy minimization for even few cycles, the disulfide bond breaks
> >> which is not expected.
> >
> > Bonds do not break in classical molecular mechanics.  One of two things is
> > happening:
> >
> > 1. There was never a bond to begin with (check your topology)
> There do a bond exists.
> 

So you can see in your [bonds] section an entry for the two atom numbers?


> 
> > 2. The bond is highly strained, in which case something is wrong with your
> > structure.
> >
> >> i have applied amber99 force field and prepared the system. while i
> >> tried
> >> with another force field in Gromacs which did not worked at all.
> >
> > What does that mean?  What failed?
> As said previously the bond is strained only after pdb2gmx itself. is
> there any other way to fix it.
> 

Previously you said the bond was strained after EM. pdb2gmx is not capable of 
straining a bond.

Be sure you are not looking at "bonds" generated via heuristics in some 
visualization program. If pdb2gmx is generating a disulfide bond, it will say 
so in the standard output, and you will be able to find it in the [bonds] 
section. Otherwise, there is no bond.

Mark


> but in gendral the molecule is free from strains.
> >
> >> also i have tried by editing specbond.dat as well but of no use.
> >
> > In what way?  Have you seen the information at:
> >
> > http://www.gromacs.org/Documentation/File_Formats/specbond.dat
> >
> 
> i tried to alter the distance of cys bond length by +/-.
>  reg,
> Parthi.
> 
> > -Justin
> >
> >> can any one share/discuss some ideas how to fix this.
> >>
> >> reg's,
> >> Parthiban.
> >>
> 
> 
> -- 
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>
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Re: [gmx-users] Re: Problem in Disulfide Bond

2011-01-20 Thread Oliver Grant

Show us that part of your topology. When you used ffamberports have you
renamed the CYS to CYS2?

Oliver

On 20 January 2011 09:23,  wrote:

> > Message: 5
> > Date: Wed, 19 Jan 2011 08:37:20 -0500
> > From: "Justin A. Lemkul" 
> > Subject: Re: [gmx-users] Re: Problem in Disulfide Bond
> > To: Discussion list for GROMACS users 
> > Message-ID: <4d36e910.6030...@vt.edu>
> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> >
> >
> >
> > parthi...@ncbs.res.in wrote:
> >> Hi
> >>
> >> I am using a dimer for my simulation system which is connected by 2
> >> disulfide bonds.
> >> After energy minimization for even few cycles, the disulfide bond breaks
> >> which is not expected.
> >
> > Bonds do not break in classical molecular mechanics.  One of two things
> is
> > happening:
> >
> > 1. There was never a bond to begin with (check your topology)
> There do a bond exists.
> > 2. The bond is highly strained, in which case something is wrong with
> your
> > structure.
> >
> >> i have applied amber99 force field and prepared the system. while i
> >> tried
> >> with another force field in Gromacs which did not worked at all.
> >
> > What does that mean?  What failed?
> As said previously the bond is strained only after pdb2gmx itself. is
> there any other way to fix it.
>
> but in gendral the molecule is free from strains.
> >
> >> also i have tried by editing specbond.dat as well but of no use.
> >
> > In what way?  Have you seen the information at:
> >
> > http://www.gromacs.org/Documentation/File_Formats/specbond.dat
> >
>
> i tried to alter the distance of cys bond length by +/-.
>  reg,
> Parthi.
>
> > -Justin
> >
> >> can any one share/discuss some ideas how to fix this.
> >>
> >> reg's,
> >> Parthiban.
> >>
>
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
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[gmx-users] glycam amber in gromacs mixed 1-4 scaling glycam06 fudgeQQ pairs coulomb amberports

2011-01-20 Thread Oliver Grant

Hi all,

I currently mix GLYCAM and AMBER in gromacs4.0.7 using the amberports and
amb2gmx.pl for the glycan. My problem is that I can't mix the scaling
properly as required for correct rotamer population sampling of the glycan
with the protein present.

>From Glycam_06g.dat:
"Correct rotational behavior for O-C-C-O fragments requires SCEE=SCNB=1.0.
This is in contrast to "standard" AMBER, in which it is normal to set
SCEE=1.2 and SCNB=2.0.  Unless you are attempting to generate rotamer
populations, it is OK to use the "standard" values.  Using non-standard
values (SCEE=SCNB=1.0) may be unacceptable when a protein is also present."

So in gromacs GLYCAM requires a fudgeQQ = 1.0 and a fudgeLJ = 1.0 whereas
the ffamberports requires fudgeQQ = 0.8333 and a fudgeLJ = 0.5.
I've been reading the mailing list archive and chris neale's method from
2006 for combining the Berger lipids and OPLS-AA forcefields however, as he
states, the method won't work in this case as the ratio of the fudgeQQ
factors is not an integer.

My understanding was that it is not possible at the minute to do this
correctly in gromacs. It would require a [ pairtypes ] section for 1-4
coulomb interactions. However I found this discussion from 2008:
http://dev-archive.ambermd.org/200812/.html

The relevant part being:
"we're chatting about implementing mixed 1-4 scaling in gromacs. It's easy
to enable on a per-molecule basis.  Enabling on a per-residue and per-atom
basis is certainly possible, but there are a bunch of ways to do it."

So... Is it currently possible to implement mixed 1-4 scaling on a
per-molecule basis? I've checked the 4.5.3 manual but it seems not to have
changed since 4.

Thanks,

Oliver
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[gmx-users] Re: Problem in Disulfide Bond

2011-01-20 Thread parthiban

> Message: 5
> Date: Wed, 19 Jan 2011 08:37:20 -0500
> From: "Justin A. Lemkul" 
> Subject: Re: [gmx-users] Re: Problem in Disulfide Bond
> To: Discussion list for GROMACS users 
> Message-ID: <4d36e910.6030...@vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> parthi...@ncbs.res.in wrote:
>> Hi
>>
>> I am using a dimer for my simulation system which is connected by 2
>> disulfide bonds.
>> After energy minimization for even few cycles, the disulfide bond breaks
>> which is not expected.
>
> Bonds do not break in classical molecular mechanics.  One of two things is
> happening:
>
> 1. There was never a bond to begin with (check your topology)
There do a bond exists.
> 2. The bond is highly strained, in which case something is wrong with your
> structure.
>
>> i have applied amber99 force field and prepared the system. while i
>> tried
>> with another force field in Gromacs which did not worked at all.
>
> What does that mean?  What failed?
As said previously the bond is strained only after pdb2gmx itself. is
there any other way to fix it.

but in gendral the molecule is free from strains.
>
>> also i have tried by editing specbond.dat as well but of no use.
>
> In what way?  Have you seen the information at:
>
> http://www.gromacs.org/Documentation/File_Formats/specbond.dat
>

i tried to alter the distance of cys bond length by +/-.
 reg,
Parthi.

> -Justin
>
>> can any one share/discuss some ideas how to fix this.
>>
>> reg's,
>> Parthiban.
>>


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[gmx-users] Re: gmx-users Digest, Vol 81, Issue 126

2011-01-20 Thread parthiban

> Message: 5
> Date: Wed, 19 Jan 2011 08:37:20 -0500
> From: "Justin A. Lemkul" 
> Subject: Re: [gmx-users] Re: Problem in Disulfide Bond
> To: Discussion list for GROMACS users 
> Message-ID: <4d36e910.6030...@vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> parthi...@ncbs.res.in wrote:
>> Hi
>>
>> I am using a dimer for my simulation system which is connected by 2
>> disulfide bonds.
>> After energy minimization for even few cycles, the disulfide bond breaks
>> which is not expected.
>
> Bonds do not break in classical molecular mechanics.  One of two things is
> happening:
>
> 1. There was never a bond to begin with (check your topology)
There do a bond exists.
> 2. The bond is highly strained, in which case something is wrong with your
> structure.
>
>> i have applied amber99 force field and prepared the system. while i
>> tried
>> with another force field in Gromacs which did not worked at all.
>
> What does that mean?  What failed?
As said previously the bond is strained only after pdb2gmx itself. is
there any other way to fix it.

but in gendral the molecule is free from strains.
>
>> also i have tried by editing specbond.dat as well but of no use.
>
> In what way?  Have you seen the information at:
>
> http://www.gromacs.org/Documentation/File_Formats/specbond.dat
>

i tried to alter the distance of cys bond length by +/-.
 reg,
Parthi.

> -Justin
>
>> can any one share/discuss some ideas how to fix this.
>>
>> reg's,
>> Parthiban.
>>

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Re: [gmx-users] running a crashed run