[gmx-users] Fwd: Question on Gromacs: rlist, rvdw, rcoulomb

[David van der Spoel]

I am a user of gromacs. I am quite confused when I came across the
relation of rlist and rvdw / rcoulomb in vdw and coulomb calculation.

In cut-off, it says rvdw / rcoulomb should be greater than rlist, while
in switch/shift, it says rvdw should be smaller than rlist...

I guess in cut-off, it's to get all the updated atoms in the calculation
of vdw/ coulomb by setting rvdw/ rcoulomb greater, but why it's the
opposite in switch...

Could you help me to understand how it's done? Thanks a lot.

Best,

Qin
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[gmx-users] re: extending the simulation

[bharat gupta]

Hi,

I extended by 3ns simulation by 2 more ns ... i.e total 5 ns but the .xtc
file shows only the 3ns trajectories and after checking the md.log file ,
its showing that it completed those 2 ns steps also... then how can I get
the trajectory for those 2ns ... I used the following commands for extending
the simulation ...

tpbconv -s previous.tpr -extend timetoextendby -o next.tpr
mdrun -s next.tpr -cpi previous.cpt

-- 
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Re: [gmx-users] crashed simulation: simulation of docked proteins in spc water crashes with LINCS warning

[Mark Abraham]

On 11/02/2011 3:47 PM, Sanjay Kumar Upadhyay wrote:


Dear gmx-users
I am experiencing some problems running a protein-protein docked
structures in water(GROMOS43a1/SPC)with gmx-4.0.4 using 8 CPUs.

I have 20 docked (protein-protein) structures of one common protein with
two different homologous protein, 10 from each group and started
simulations for all, using same parameters.

I did energy minimization for all the systems, all systems reached to
energy minimized configuration in between 1 to 12000 steps using steep
algorithm and PE for all minimized systems are vary between -3975853 to
-3571906 KJ/mol.

In final MD out off 10 simulations 9 from each group was crassed in
between 200 ps to 900 ps with lincs warning. However one simulation from
each group running well up to 5 ns, and after 5ns out of these two, one
simulation crassed with too many lincs warning, while other one completed
20ns and steel continue.


It sounds like you are not using a proper equilibration protocol before 
attempting to run MD. Occasionally that can work, but often it doesn't. 
See 
http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation


Mark


when restarting the *crashed *simulation feeding "-cpi md.cpt" to mdrun
the simulation restarts fine with few steps before but stopped at same
portion of the simulation with same lincs warning. I checked the energy
and temperature distribution and find that potential energy is
fine,however total energy of systems as well as temperature (300K attain
321K
at last steps) is higher at last steps before simulation stops.I read
all the mailing least before posting this question but did not reach any
conclusion. Any explanation or solution for this, why one simulation is
stable and running fine up to more than 20ns however others are crassed
with same parameters?? I am thinking that it may be because of steric
class between docked protein. Is it mean that one docked structure making
more
natural interaction in compare to other docked structures???


  Regards
  Sanjay Kumar Upadhyay
  Research Scholor
  Protein Dynamics lab
  Dept of Chemistry
  IIT Powai, Mumbai, 400076
  Ph no. 09920200345, 09699353562,






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Re: [gmx-users] More than one settle type.

[Mark Abraham]

On 11/02/2011 2:50 PM, Sikandar Mashayak wrote:

Hi

I am performing SPC/E water simulation where I want to fix location of 
one water molecule and let others move. To do that I have defined two 
groups with name SOL0 and SOL, where SOL0 has just one water molecule 
and SOL grp contains all others. In .mdp file I define freezegrps as 
SOL0 . When I do the simulation by mdrun I get error that "More than 
one settle type.". I understand this means, I can not have two 
molecules with [settle] constraints, I will have define [constraint] 
for one SPC/E molecule explicitly. Can anyone please suggest me how to 
do it?


I think you haven't quite understood the error, but I haven't got enough 
information to be sure. The error says that your topology cannot specify 
two molecule *types* with [ settle ] blocks. Where you say "groups" 
above, I think you mean "molecule blocks". The former are specified in 
an index file (and generated by default if no index file is used), and 
the latter in the [ molecules ] section of your topology. The two are 
unrelated. See this thread from just a fortnight ago 
http://lists.gromacs.org/pipermail/gmx-users/2011-January/057966.html. 
Searching for answers first before emailing is often educational :-).


Mark
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[gmx-users] crashed simulation: simulation of docked proteins in spc water crashes with LINCS warning

[Sanjay Kumar Upadhyay]

Dear gmx-users
I am experiencing some problems running a protein-protein docked
structures in water(GROMOS43a1/SPC)with gmx-4.0.4 using 8 CPUs.

I have 20 docked (protein-protein) structures of one common protein with
two different homologous protein, 10 from each group and started
simulations for all, using same parameters.

I did energy minimization for all the systems, all systems reached to
energy minimized configuration in between 1 to 12000 steps using steep
algorithm and PE for all minimized systems are vary between -3975853 to
-3571906 KJ/mol.

In final MD out off 10 simulations 9 from each group was crassed in
between 200 ps to 900 ps with lincs warning. However one simulation from
each group running well up to 5 ns, and after 5ns out of these two, one
simulation crassed with too many lincs warning, while other one completed
20ns and steel continue.

when restarting the *crashed *simulation feeding "-cpi md.cpt" to mdrun
the simulation restarts fine with few steps before but stopped at same
portion of the simulation with same lincs warning. I checked the energy
and temperature distribution and find that potential energy is
fine,however total energy of systems as well as temperature (300K attain
321K
at last steps) is higher at last steps before simulation stops.I read
all the mailing least before posting this question but did not reach any
conclusion. Any explanation or solution for this, why one simulation is
stable and running fine up to more than 20ns however others are crassed
with same parameters?? I am thinking that it may be because of steric
class between docked protein. Is it mean that one docked structure making
more
natural interaction in compare to other docked structures???


 Regards
 Sanjay Kumar Upadhyay
 Research Scholor
 Protein Dynamics lab
 Dept of Chemistry
 IIT Powai, Mumbai, 400076
 Ph no. 09920200345, 09699353562,




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[gmx-users] More than one settle type.

[Sikandar Mashayak]

Hi

I am performing SPC/E water simulation where I want to fix location of one
water molecule and let others move. To do that I have defined two groups
with name SOL0 and SOL, where SOL0 has just one water molecule and SOL grp
contains all others. In .mdp file I define freezegrps as SOL0 . When I do
the simulation by mdrun I get error that "More than one settle type.". I
understand this means, I can not have two molecules with [settle]
constraints, I will have define [constraint] for one SPC/E molecule
explicitly. Can anyone please suggest me how to do it?

thanks
sikandar
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[gmx-users] Problem with Gromacs Installation

[majid hasan]

Dear All,

I installed gromacs-4.5.3 using cygwin on windows 7, following the instructions 
on http://www.gromacs.org/Downloads/Installation_Instructions/Cygwin_HOWTO. 
However, after installation, when I tried to run gromacs, I couldn't find the 
"share" folder in D:/cygwin/usr/local/gromacs. This share folder contains the 
"demo" that I was trying to run. I only see "bin", "include", and "lib" folders 
in gromacs. Could anyone please help me with this?

Thanks,
Majid


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RE: [gmx-users] Dangling phospholipids

[Dallas Warren]

Or it could be a PBC issue, that sections of chain that appear to be dangling 
out into space actually enter the other side of the box.

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. 


> -Original Message-
> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-
> boun...@gromacs.org] On Behalf Of Justin A. Lemkul
> Sent: Thursday, 10 February 2011 4:26 AM
> To: ra...@fis.unam.mx; Discussion list for GROMACS users
> Subject: Re: [gmx-users] Dangling phospholipids
> 
> 
> 
> Dr. Ramón Garduño-Juárez wrote:
> > Dear All,
> >
> > First of all I want to tank Justin Lemkul and Thomas Piggot for their
> > useful comments that helped me to resolve my previous questions
> > regarding the construction of a lipid membrane.
> >
> > Now I would like to post this question to this forum.
> >
> > I got through placing a putative ion channel into a DPPC bilayer. I
> > managed to expand this sytem -> minimize it -> shrink it (several
> times)
> > -> minimize it (several times) until I got an adequate lipid density.
> >
> > After viewing the final results I noticed that there are several
> lipid
> > molecules that are dangling at the end of the periodic box.
> >
> > Is this normal, or I did something wrong?. If this is expected, How
> do I
> > get rid of the dangling lipid molecules before I start a MD
> simulation?
> >
> 
> By "dangling" do you mean that they are somewhat isolated from the rest
> of the
> lipids?  If so, how many are there?  Usually this just indicates that
> you're not
> done shrinking the membrane back to appropriate dimensions.  The final
> box
> vectors achieved through shrinking should usually be fairly close to
> the
> original dimensions of the system.  If this is not the case, then
> you're not
> done building your system.
> 
> -Justin
> 
> > Waiting for your replies...
> >
> > Sincerely,
> > 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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Re: [gmx-users] localpressure.dat file not created

[Justin A. Lemkul]

ma...@physics.ucsb.edu wrote:

On 10/02/2011 11:48 AM, ma...@physics.ucsb.edu wrote:

I successfully ran version 4.5.3 to simulate a small DPPC bilayer patch
using the files from Marrink's website by typing:

/usr/bin/grompp -v -f mem.mdp -c mem.gro -p mem.top -o topol.tpr
-maxwarn 100

mdrun

In the .mdp file I then added the line "userreal1=0.1" and typed

/usr/bin/grompp_d -v -f mem.mdp -c mem.gro -p mem.top -o topol.tpr
-maxwarn 100

mdrun_d -rerun traj.xtc -v

Everything ran smoothly, but I don't see any localpressure.dat file
sitting in my directory. How can I get it?

AFAIK there's no port of the "local pressure" variant of GROMACS to
4.5.3. You haven't told us whether you think you have one.

Mark


I don't know if I have a port of the local pressure variant. How do I find


If you have to ask, odds are you aren't using it :)


out? Or, what version of GROMACS is more compatible with the local
pressure variant?



You can get snapshot releases from the online git repo:

http://repo.or.cz/w/gromacs.git/shortlog/refs/heads/release-4-5-localpressure

or the 4.0 version:

http://repo.or.cz/w/gromacs.git/shortlog/refs/heads/localpressure-4-0

I am not aware of the stability or suitability of either of these branches; 
perhaps one of the developers can comment.  But the online repo is the only 
place I know of where one can obtain a reasonably modern version of the 
localpressure extension.


-Justin


Thanks!

--Max


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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] localpressure.dat file not created

[maxcw]

> On 10/02/2011 11:48 AM, ma...@physics.ucsb.edu wrote:
>> I successfully ran version 4.5.3 to simulate a small DPPC bilayer patch
>> using the files from Marrink's website by typing:
>>
>> /usr/bin/grompp -v -f mem.mdp -c mem.gro -p mem.top -o topol.tpr
>> -maxwarn 100
>>
>> mdrun
>>
>> In the .mdp file I then added the line "userreal1=0.1" and typed
>>
>> /usr/bin/grompp_d -v -f mem.mdp -c mem.gro -p mem.top -o topol.tpr
>> -maxwarn 100
>>
>> mdrun_d -rerun traj.xtc -v
>>
>> Everything ran smoothly, but I don't see any localpressure.dat file
>> sitting in my directory. How can I get it?
>
> AFAIK there's no port of the "local pressure" variant of GROMACS to
> 4.5.3. You haven't told us whether you think you have one.
>
> Mark

I don't know if I have a port of the local pressure variant. How do I find
out? Or, what version of GROMACS is more compatible with the local
pressure variant?

Thanks!

--Max

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>


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Re: [gmx-users] rotamers during minimization

[Justin A. Lemkul]

abdullah ahmed wrote:
Hello, 

I would like to know if gromacs is designed to try and keep as close to 
the original structure as much as possible? 


All motions are governed by the potential energy functions for bonded and 
nonbonded interactions.  Gromacs is not biased towards keeping certain 
configurations.  EM generally does not make very large changes, and is designed 
only to optimize a structure such that it can be used stably during MD.  Since 
you're not dealing with any velocities, motions are generally very small.


After minimizing a structure with phenyl-alanines I realized that a 
better minimization could be achieved if the rotamer had been changed 
during the minimization. However I have been unable to induce gromacs to 
do this on its own during minimization. 
I could of course, change the original structure but I prefer not to. 



If EM converged to acceptable criteria, then there's no problem.  But you seem 
to think that a certain structure is "better," so you should do whatever 
achieves your goals and is scientifically sound.  If a particular rotamer truly 
is better, the structure should (in theory) adopt this position more often than 
not during MD.


-Justin

Thank you in advance, 
Abdullah Ahmed


My .mdp file is as follows: 


;
; User spoel (236)
; Wed Nov  3 17:12:44 1993
; Input file
;
;
cpp =  /usr/bin/cpp
define  =  -DPOSRES  
constraints =  none

integrator  =  steep
nsteps  =  2000
;
; Energy minimizing stuff:
;
emtol   =  0.2
emstep  =  0.001

nstcomm =  1
ns_type =  grid
rlist   =  1
rcoulomb=  1
rvdw=  1
Tcoupl  =  no
Pcoupl  =  no
gen_vel =  no



--


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] rotamers during minimization

[abdullah ahmed]

Hello, 
I would like to know if gromacs is designed to try and keep as close to the 
original structure as much as possible? After minimizing a structure with 
phenyl-alanines I realized that a better minimization could be achieved if the 
rotamer had been changed during the minimization. However I have been unable to 
induce gromacs to do this on its own during minimization. I could of course, 
change the original structure but I prefer not to. 
Thank you in advance, Abdullah Ahmed
My .mdp file is as follows: 
;;  User spoel (236);   Wed Nov  3 17:12:44 1993;   Input file;;cpp 
=  /usr/bin/cppdefine  =  -DPOSRES  constraints 
=  noneintegrator  =  steepnsteps  =  2000;; Energy 
minimizing stuff:;emtol   =  0.2emstep  =  0.001
nstcomm =  1ns_type =  gridrlist   =  
1rcoulomb=  1rvdw=  1Tcoupl  =  
noPcoupl  =  nogen_vel =  no
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Re: [gmx-users] ref_temp and gen_temp during simulated annealing

[Justin A. Lemkul]

bipin singh wrote:

Hello users,
I have some doubt regarding the reference temperature(ref_temp)option  
during simulated annealing, i mean in the .mdp for simulated annealing 
what should be the correct ref_temp i.e. 0 K(starting temerature) or the 
target temperature(328K) and accordingly what should be the value for 
gen_temp(0K or 328K).




AFAIK, ref_t is ignored during annealing, since the heating is controlled by a 
separate algorithm.  The gen_temp issue is more complex - how does one even 
represent 0 K, as the velocities are zero?  I don't know what grompp might do if 
you set "gen_temp = 0" in the .mdp file.  Try it and see.  The success or 
failure of annealing will be very obvious, even with a short simulation.


-Justin


The part of my mdp file for the simulated annealing is as follows:

;Annealing
annealing=single
annealing_temp=0 20 40 60 80 100 120 140 160 180 200 220 240 260 280 300 
320 328

annealing_npoints=18
annealing_time=0 20 40 60 80 100 120 140 160 180 200 220 240 260 280 300 
320 340

;Temperature coupling is on in two groups
Tcoupl= V-rescale
tau_t= 0.1
tc-grps= System
ref_t= 328
pbc= xyz   ; 3-D PBC
; Pressure coupling is off
pcoupl  = no ; no pressure coupling in NVT
compressibility= 4.5e-5
; Generate velocites is on at 328 K.
gen_vel= yes ; assign velocities from Maxwell distribution
gen_temp= 328.0 ; temperature for Maxwell distribution
gen_seed= 173529;generate a random seed


--
/
-
Thanks and regards
/Bipin Singh/
/
/
/



--


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] ref_temp and gen_temp during simulated annealing

[bipin singh]

Hello users,
I have some doubt regarding the reference temperature(ref_temp)option
during simulated annealing, i mean in the .mdp for simulated annealing what
should be the correct ref_temp i.e. 0 K(starting temerature) or the target
temperature(328K) and accordingly what should be the value for gen_temp(0K
or 328K).

The part of my mdp file for the simulated annealing is as follows:

;Annealing
annealing=single
annealing_temp=0 20 40 60 80 100 120 140 160 180 200 220 240 260 280 300 320
328
annealing_npoints=18
annealing_time=0 20 40 60 80 100 120 140 160 180 200 220 240 260 280 300 320
340
;Temperature coupling is on in two groups
Tcoupl= V-rescale
tau_t= 0.1
tc-grps= System
ref_t= 328
pbc= xyz   ; 3-D PBC
; Pressure coupling is off
pcoupl  = no ; no pressure coupling in NVT
compressibility= 4.5e-5
; Generate velocites is on at 328 K.
gen_vel= yes ; assign velocities from Maxwell distribution
gen_temp= 328.0 ; temperature for Maxwell distribution
gen_seed= 173529;generate a random seed


-- 
*
-
Thanks and regards
Bipin Singh
*
*
*
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Re: [gmx-users] PRODRG

[Justin A. Lemkul]

mohsen ramezanpour wrote:

Dear Dr.Justin

I have read this section before.
There are 2 problem:
1:ADDHYD atomname and DELHYD atomname  commands dosen't work!
they result in ERROR in PRODRG



You have to run PRODRG twice.  The first time, you get the wrong output.  Note 
the atom name that PRODRG assigns to your N atom.  The second time, use DELHYD 
(name).  If that doesn't work, then I have no idea and you're better off 
submitting your question to the PRODRG developers.



2:Actually I don't know the additional hydrogen is necessary or not!
Because it may be necessary for proper protonation.
My drug(Sertraline) is in a solvent,it may interact with water molecules 
and Nitrogen may  get an additional hydrogen.




A doubly-protonated secondary amine would be a fairly strong acid.  You should 
do a pKa calculation to determine what is relevant rather than guessing.  There 
are web servers and other software out there that can do this for you.  Google 
is your friend.


-Justin


What do you think?


On Wed, Feb 9, 2011 at 9:39 PM, Justin A. Lemkul > wrote:



The OP's question is easily answered by referring to the PRODRG FAQ
in dealing with proper protonation.

As for Antechamber and the like, these are good tools, but do not
produce GROMOS-compatible topologies, if that is indeed the
underlying goal.  We've done thorough analysis of various QM
calculation methods for GROMOS charges, and none of them produce
completely satisfactory topologies.  Antechamber, Spartan, Gaussian,
etc are good for initial charge calculations, but IMHO do not
qualify as an "end result" for GROMOS parameterization due to the
empirical refinement used in the force field derivation.  All of
that makes GROMOS parameterization somewhat tricky, and hence why
force field choice is so incredibly important when designing
projects... ;)

-Justin


TJ Mustard wrote:



Yes I would recommend acpype.

On February 9, 2011 at 9:42 AM
jorge_quint...@ciencias.uis.edu.co
 wrote:

 > I think that is better to use antechamber tools.
 >
 >
 > > On 10/02/2011 3:40 AM, mohsen ramezanpour wrote:
 > >> Dear Users
 > >>
 > >> I am using PRODRG to make topology for my drug
 > >> It addes Hydrogenes but in wrong way.
 > >> My Nitrogen atom is bonded to 2 Carbos,
 > >> and PRODRG addes 2 Hydrogenes to it .
 > >> Please let me know how can I do.
 > >> Thanks in advance
 > >
 > > This is not really the forum to get help about that. You
need to read
 > > how to PRODRG needs input, and supply something it can deal
with. Then
 > > do a whole bunch more work testing what it produced.
 > >
 > > Mark
 > > --
 > > gmx-users mailing listgmx-users@gromacs.org

 > > http://lists.gromacs.org/mailman/listinfo/gmx-users
 > > Please search the archive at
 > > http://www.gromacs.org/Support/Mailing_Lists/Search before
posting!
 > > Please don't post (un)subscribe requests to the list. Use the
 > > www interface or send it to gmx-users-requ...@gromacs.org
.
 > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
 > >
 >
 >
 > --
 > Jorge R. Quintero
 > Químico
 > Universidad Industrial de Santander
 > Bucaramanga, Santander - Colombia
 >
 > --
 > 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
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.
 > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
 >

 
TJ Mustard

Email: musta...@onid.orst.edu 


-- 



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] PRODRG

[mohsen ramezanpour]

Dear Dr.Justin

I have read this section before.
There are 2 problem:
1:ADDHYD atomname and DELHYD atomname  commands dosen't work!
they result in ERROR in PRODRG

2:Actually I don't know the additional hydrogen is necessary or not!
Because it may be necessary for proper protonation.
My drug(Sertraline) is in a solvent,it may interact with water molecules and
Nitrogen may  get an additional hydrogen.

What do you think?


On Wed, Feb 9, 2011 at 9:39 PM, Justin A. Lemkul  wrote:

>
> The OP's question is easily answered by referring to the PRODRG FAQ in
> dealing with proper protonation.
>
> As for Antechamber and the like, these are good tools, but do not produce
> GROMOS-compatible topologies, if that is indeed the underlying goal.  We've
> done thorough analysis of various QM calculation methods for GROMOS charges,
> and none of them produce completely satisfactory topologies.  Antechamber,
> Spartan, Gaussian, etc are good for initial charge calculations, but IMHO do
> not qualify as an "end result" for GROMOS parameterization due to the
> empirical refinement used in the force field derivation.  All of that makes
> GROMOS parameterization somewhat tricky, and hence why force field choice is
> so incredibly important when designing projects... ;)
>
> -Justin
>
>
> TJ Mustard wrote:
>
>>
>>
>> Yes I would recommend acpype.
>>
>> On February 9, 2011 at 9:42 AM jorge_quint...@ciencias.uis.edu.co wrote:
>>
>>  > I think that is better to use antechamber tools.
>>  >
>>  >
>>  > > On 10/02/2011 3:40 AM, mohsen ramezanpour wrote:
>>  > >> Dear Users
>>  > >>
>>  > >> I am using PRODRG to make topology for my drug
>>  > >> It addes Hydrogenes but in wrong way.
>>  > >> My Nitrogen atom is bonded to 2 Carbos,
>>  > >> and PRODRG addes 2 Hydrogenes to it .
>>  > >> Please let me know how can I do.
>>  > >> Thanks in advance
>>  > >
>>  > > This is not really the forum to get help about that. You need to read
>>  > > how to PRODRG needs input, and supply something it can deal with.
>> Then
>>  > > do a whole bunch more work testing what it produced.
>>  > >
>>  > > Mark
>>  > > --
>>  > > gmx-users mailing listgmx-users@gromacs.org
>>  > > http://lists.gromacs.org/mailman/listinfo/gmx-users
>>  > > Please search the archive at
>>  > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>  > > Please don't post (un)subscribe requests to the list. Use the
>>  > > www interface or send it to gmx-users-requ...@gromacs.org.
>>  > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>  > >
>>  >
>>  >
>>  > --
>>  > Jorge R. Quintero
>>  > Químico
>>  > Universidad Industrial de Santander
>>  > Bucaramanga, Santander - Colombia
>>  >
>>  > --
>>  > 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
>>  >
>>
>>
>> TJ Mustard
>> Email: musta...@onid.orst.edu
>>
>>
> --
> 
>
> 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
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Re: [gmx-users] Re: server_for_Gaussian

[Diego Enry]

You can benefit from the WebMO server. It will not run very
"expensive" jobs but is a handy !

http://www.webmo.net/

Support for Gamess 1999+, Gaussian 94/98/03/09, MolPro 2002/2006/2009,
Mopac 7/93/200X, NWChem 4/5, PQS 3.3, PSI 3+, QChem 2/3, and Tinker
4/5

On Thu, Feb 10, 2011 at 12:43 PM, Thomas Schlesier  wrote:
>
>>
>> Message: 2
>> Date: Thu, 10 Feb 2011 16:10:45 +0530
>> From: shahid nayeem
>> Subject: [gmx-users] server_for_Gaussian
>> To: Discussion list for GROMACS users
>> Message-ID:
>>        
>> Content-Type: text/plain; charset=ISO-8859-1
>>
>> Dear All
>>
>> If any one is aware of a server on which one can upload job for
>> running Gaussian, Please let me know. This I need to modify charges in
>>  the topology file created by ProDrg server.
>> Shahid Nayeem
>>
>
> here is one:
> http://q4md-forcefieldtools.org/REDS/
> you can also directly calculated there resp charges. But if you use resp
> charges, it would be better to also change the force-field (since
> gromos-ff's are for their empirical charges and not resp-charges).
> you could use for example amber's gaff force-field, which uses resp charges.
> see amber/gaff page for more information.
>
> greetings
> thomas
> --
> gmx-users mailing list    gmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
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>



-- 
Diego Enry B. Gomes
Laboratório de Modelagem e Dinamica Molecular
Universidade Federal do Rio de Janeiro - Brasil.

/home/temp @ Ecole Normale Superieure de Cachan, France
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Re: [gmx-users] WHAM with multiple force constants

[XAvier Periole]

On Feb 10, 2011, at 3:08 PM, jk...@ifr88.cnrs-mrs.fr wrote:


Hi,

I'm running an Umbrella Sampling analysis, with 1A steps in the  
reaction coordinate (distance) to estimate a PMF. However, owing to  
(high?) energetic barriers between my two proteins, some coordinates  
are not sampled. I intend to run simulations with stronger force  
constants to prevent my protein from fleeing to the nearest  
energetic minima.


So my question is : does  using different force constants to  
restrain the distance between my two proteins influences the PMF  
estimated by g_wham ?

No it does not assuming each window is equilibrated.


From what I understood, it doesn't seems so, as long as the  
distributions are well overlapped. But since I intend to invest a  
considerable amount of CPU time, a confirmation would be really  
apreciated !


Thanks,

Jonathan.




--
Message envoyé via le Webmail de l'IFR88 (http://www.ifr88.cnrs- 
mrs.fr).



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[gmx-users] WHAM with multiple force constants

[jkhao]

Hi,

I'm running an Umbrella Sampling analysis, with 1A steps in the  
reaction coordinate (distance) to estimate a PMF. However, owing to  
(high?) energetic barriers between my two proteins, some coordinates  
are not sampled. I intend to run simulations with stronger force  
constants to prevent my protein from fleeing to the nearest energetic  
minima.


So my question is : does  using different force constants to restrain  
the distance between my two proteins influences the PMF estimated by  
g_wham ?


From what I understood, it doesn't seems so, as long as the  
distributions are well overlapped. But since I intend to invest a  
considerable amount of CPU time, a confirmation would be really  
apreciated !


Thanks,

Jonathan.




--
Message envoyé via le Webmail de l'IFR88 (http://www.ifr88.cnrs-mrs.fr).


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Re: [gmx-users] Error: No such moleculetype Protein

[Anirban Ghosh]

Hi,

I have worked around the problem. I was not including a .itp file. But now I
am getting Segmentation Fault:

Excluding 1 bonded neighbours for DSPC 104
Excluding 1 bonded neighbours for W 1397
Excluding 1 bonded neighbours for NA+ 0
Excluding 1 bonded neighbours for CL- 4

Number of fg atoms 410288
Number of cg atoms 57296
Reading frames from gro file 'Protein in DSPC Bilayer', 57296 atoms.
Reading frame   0 time0.000   1297343010
Segmentation fault


Why is this happening?


Thanks,

Anirban


On Thu, Feb 10, 2011 at 5:45 PM, Anirban Ghosh <
reach.anirban.gh...@gmail.com> wrote:

> Hi Tsjerk,
>
> Thanks for the reply.
> Yes, I had a reference to 'Protein' group in my .mdp file while running the
> CGMD. Now, after CG run I am trying to convert the CG to FG model using:
>
> g_fg2cg -pfg topol_fg.top -pcg system_cg.top -n 0 -c cg.gro -o fg.gro
>
> So do I need to supply any other parameter to this command or how to
> mention this refering of 'Protein' group here.
>
> Thanks,
>
> Anirban
>
>
>
> On Thu, Feb 10, 2011 at 5:28 PM, Tsjerk Wassenaar wrote:
>
>> Hi Anirban,
>>
>> Probably you have a reference to a group 'Protein' in your .mdp file.
>>
>> Cheers,
>>
>> Tsjerk
>>
>> On Thu, Feb 10, 2011 at 12:01 PM, Anirban Ghosh
>>  wrote:
>> > Hi,
>> > I am trying to convert a CG system containing multiple copies of a
>> protein +
>> > lipid + water + ions to an all-atom system using the special
>> gromacs_reverse
>> > version command g_fg2cg. However I am getting the error:
>> >
>> ---
>> > calling cpp...
>> > processing topology...
>> > Generated 4 of the 780 non-bonded parameter combinations
>> > Cleaning up temporary file grompp9YJMaA
>> > ---
>> > Program g_fg2cg, VERSION 3.3.1
>> > Source code file: ../kernel/toppush.c, line: 1293
>> > Fatal error:
>> > No such moleculetype Protein
>> >
>> -
>> > I have checked all the include statements and .itp files, but cannot fix
>> the
>> > issue. Is seems to be very trivial but still exists.
>> > Any suggestion is welcome.
>> >
>> > Thanks,
>> > Anirban
>> > --
>> > 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
>> >
>>
>>
>>
>> --
>> Tsjerk A. Wassenaar, Ph.D.
>>
>> post-doctoral researcher
>> Molecular Dynamics Group
>> * Groningen Institute for Biomolecular Research and Biotechnology
>> * Zernike Institute for Advanced Materials
>> University of Groningen
>> The Netherlands
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>
>
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Re: [gmx-users] Error: No such moleculetype Protein

[Anirban Ghosh]

Hi Tsjerk,

Thanks for the reply.
Yes, I had a reference to 'Protein' group in my .mdp file while running the
CGMD. Now, after CG run I am trying to convert the CG to FG model using:

g_fg2cg -pfg topol_fg.top -pcg system_cg.top -n 0 -c cg.gro -o fg.gro

So do I need to supply any other parameter to this command or how to mention
this refering of 'Protein' group here.

Thanks,

Anirban



On Thu, Feb 10, 2011 at 5:28 PM, Tsjerk Wassenaar  wrote:

> Hi Anirban,
>
> Probably you have a reference to a group 'Protein' in your .mdp file.
>
> Cheers,
>
> Tsjerk
>
> On Thu, Feb 10, 2011 at 12:01 PM, Anirban Ghosh
>  wrote:
> > Hi,
> > I am trying to convert a CG system containing multiple copies of a
> protein +
> > lipid + water + ions to an all-atom system using the special
> gromacs_reverse
> > version command g_fg2cg. However I am getting the error:
> >
> ---
> > calling cpp...
> > processing topology...
> > Generated 4 of the 780 non-bonded parameter combinations
> > Cleaning up temporary file grompp9YJMaA
> > ---
> > Program g_fg2cg, VERSION 3.3.1
> > Source code file: ../kernel/toppush.c, line: 1293
> > Fatal error:
> > No such moleculetype Protein
> >
> -
> > I have checked all the include statements and .itp files, but cannot fix
> the
> > issue. Is seems to be very trivial but still exists.
> > Any suggestion is welcome.
> >
> > Thanks,
> > Anirban
> > --
> > 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
> >
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Molecular Dynamics Group
> * Groningen Institute for Biomolecular Research and Biotechnology
> * Zernike Institute for Advanced Materials
> University of Groningen
> The Netherlands
> --
> gmx-users mailing listgmx-users@gromacs.org
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Re: [gmx-users] Error: No such moleculetype Protein

[Tsjerk Wassenaar]

Hi Anirban,

Probably you have a reference to a group 'Protein' in your .mdp file.

Cheers,

Tsjerk

On Thu, Feb 10, 2011 at 12:01 PM, Anirban Ghosh
 wrote:
> Hi,
> I am trying to convert a CG system containing multiple copies of a protein +
> lipid + water + ions to an all-atom system using the special gromacs_reverse
> version command g_fg2cg. However I am getting the error:
> ---
> calling cpp...
> processing topology...
> Generated 4 of the 780 non-bonded parameter combinations
> Cleaning up temporary file grompp9YJMaA
> ---
> Program g_fg2cg, VERSION 3.3.1
> Source code file: ../kernel/toppush.c, line: 1293
> Fatal error:
> No such moleculetype Protein
> -
> I have checked all the include statements and .itp files, but cannot fix the
> issue. Is seems to be very trivial but still exists.
> Any suggestion is welcome.
>
> Thanks,
> Anirban
> --
> gmx-users mailing list    gmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>



-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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[gmx-users] Re: server_for_Gaussian

[Thomas Schlesier]

Message: 2
Date: Thu, 10 Feb 2011 16:10:45 +0530
From: shahid nayeem
Subject: [gmx-users] server_for_Gaussian
To: Discussion list for GROMACS users
Message-ID:

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

Dear All

If any one is aware of a server on which one can upload job for
running Gaussian, Please let me know. This I need to modify charges in
  the topology file created by ProDrg server.
Shahid Nayeem



here is one:
http://q4md-forcefieldtools.org/REDS/
you can also directly calculated there resp charges. But if you use resp 
charges, it would be better to also change the force-field (since 
gromos-ff's are for their empirical charges and not resp-charges).
you could use for example amber's gaff force-field, which uses resp 
charges. see amber/gaff page for more information.


greetings
thomas
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Re: [gmx-users] server_for_Gaussian

[Justin A. Lemkul]

shahid nayeem wrote:

Dear All

If any one is aware of a server on which one can upload job for
running Gaussian, Please let me know. This I need to modify charges in
 the topology file created by ProDrg server.


Gaussian is commercial software.  Making is available freely to the public is 
probably a violation of their license.


-Justin


Shahid Nayeem


--


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] pull code

[Justin A. Lemkul]

Poojari, Chetan wrote:

Hi Justin,

Thank you very much for your suggestions. I will use constraint force  to
force a peptide into a membrane with pulling for longer time.

yes with "POSRES_LIPID"   i am keeping the lipids rigid while pulling the
peptide inside.  Should the lipids be flexible while pulling??



If your lipids are completely rigid, then they will not be happy accommodating 
the introduction of a peptide into that environment.



I am using pull_geometry   = direction, In the tutorial mdp file you had
commented saying cant get PMF with direction. So please can I know if this
error of not getting PMF with direction fixed or with pull_geometry   =
distance will i be able to pull the peptide into membrane with still using
pull direction pull_vec1   = 0.0 0.0 -1.0



You're not doing umbrella sampling, you're doing steered MD, which is a 
non-equilibrium process.  Please read the tutorial carefully.


-Justin





Kind regards, chetan


 From: gmx-users-boun...@gromacs.org
[gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul
[jalem...@vt.edu] Sent: 09 February 2011 16:40 To: Discussion list for
GROMACS users Subject: Re: [gmx-users] pull code

Poojari, Chetan wrote:

Hi,

I am using umbrella sampling to pull my peptide (peptide starting from
above the lipid bilayer) into the hydrophobic core of the lipid bilayer.

Following are my inputs i have used:

title   = Umbrella pulling simulation define  =
-DPOSRES_LIPID ; Run parameters integrator  = md dt  =
0.002 tinit   = 0 nsteps  = 25; 500 ps nstcomm
= 1 . . ; Pull code pull= umbrella pull_geometry   = direction 
pull_dim= N N Y pull_start  = yes   ; define initial

COM distance > 0 pull_ngroups= 1 pull_group0 = POPC pull_group1
= Protein pull_vec1   = 0.0 0.0 -1.0 pull_rate1  = 0.01  ;
0.01 nm per ps = 10 nm per ns pull_k1 = 1000  ; kJ mol^-1
nm^-2


After running the this step:  grompp -f md_pull.mdp -c npt.gro -p topol.top
-n index.ndx -t npt.cpt -o pull.tpr

i get grompp output as such:

Pull group  natoms  pbc atom  distance at start reference at t=0 0
6656  3433 1   10553  -4.132-4.132

I am starting to pull my peptide from 1nm above the upper leaf headgroup. I
am using POPC lipids and distance between 2 adjacent headgroups seem to be
around 4.2 nm.

I want the peptide to be pulled into the bilayer till the lower leaf lipid
headgroups, but the peptide is being pulled only till middle of the
hydrophobic core of the bilayer.

Please can I know what might be the problem ?



Either you're (1) not pulling for sufficient time, (2) not pulling hard
enough, or (3) the physical properties of the system don't allow for such a
position.

For (2), using a harmonic potential to try to force a peptide into a membrane
is probably not a great idea.  A constraint force is probably better.  For
(3), what does "POSRES_LIPID" refer to?  Are you keeping the lipids too rigid
by doing so?


While viewing the conf.*gro file outputed  from the traj. (after extracting
the frames), i found few lipid molecules to be broken. Please can I know if
there is a way to avoid these broken structures??? Is there a possibility
that I am not able to pull the peptide into the lower leaf head group due
to these broken lipid structures?




Please become comfortable with the concept of periodic boundary conditions.

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


-Justin



Any suggestions will be helpful.


Kind regards, chetan.


 


 Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft:
Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B
3498 Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher 
Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Dr. Ulrich

Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr.
Sebastian M. Schmidt 

 





-- 

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] Error: No such moleculetype Protein

[Anirban Ghosh]

Hi,

I am trying to convert a CG system containing multiple copies of a protein +
lipid + water + ions to an all-atom system using the special gromacs_reverse
version command g_fg2cg. However I am getting the error:

---
calling cpp...
processing topology...
Generated 4 of the 780 non-bonded parameter combinations
Cleaning up temporary file grompp9YJMaA
---
Program g_fg2cg, VERSION 3.3.1
Source code file: ../kernel/toppush.c, line: 1293

Fatal error:
No such moleculetype Protein
-

I have checked all the include statements and .itp files, but cannot fix the
issue. Is seems to be very trivial but still exists.
Any suggestion is welcome.


Thanks,

Anirban
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[gmx-users] server_for_Gaussian

[shahid nayeem]

Dear All

If any one is aware of a server on which one can upload job for
running Gaussian, Please let me know. This I need to modify charges in
 the topology file created by ProDrg server.
Shahid Nayeem
-- 
gmx-users mailing listgmx-users@gromacs.org
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RE: [gmx-users] pull code

[Poojari, Chetan]

Hi Justin,

Thank you very much for your suggestions. I will use constraint force  to force 
a peptide into a membrane with pulling for longer time. 

yes with "POSRES_LIPID"   i am keeping the lipids rigid while pulling the 
peptide inside.  Should the lipids be flexible while pulling??

I am using pull_geometry   = direction, In the tutorial mdp file you had 
commented saying cant get PMF with direction. So please can I know if this 
error of not getting PMF with direction fixed or with pull_geometry   = 
distance will i be able to pull the peptide into membrane with still using pull 
direction pull_vec1   = 0.0 0.0 -1.0




Kind regards,
chetan



From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf 
Of Justin A. Lemkul [jalem...@vt.edu]
Sent: 09 February 2011 16:40
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] pull code

Poojari, Chetan wrote:
> Hi,
>
> I am using umbrella sampling to pull my peptide (peptide starting from above 
> the lipid bilayer) into the hydrophobic core of the lipid bilayer.
>
> Following are my inputs i have used:
>
> title   = Umbrella pulling simulation
> define  = -DPOSRES_LIPID
> ; Run parameters
> integrator  = md
> dt  = 0.002
> tinit   = 0
> nsteps  = 25; 500 ps
> nstcomm = 1
> .
> .
> ; Pull code
> pull= umbrella
> pull_geometry   = direction
> pull_dim= N N Y
> pull_start  = yes   ; define initial COM distance > 0
> pull_ngroups= 1
> pull_group0 = POPC
> pull_group1 = Protein
> pull_vec1   = 0.0 0.0 -1.0
> pull_rate1  = 0.01  ; 0.01 nm per ps = 10 nm per ns
> pull_k1 = 1000  ; kJ mol^-1 nm^-2
>
>
> After running the this step:  grompp -f md_pull.mdp -c npt.gro -p topol.top 
> -n index.ndx -t npt.cpt -o pull.tpr
>
> i get grompp output as such:
>
> Pull group  natoms  pbc atom  distance at start reference at t=0
>0  6656  3433
>1   10553  -4.132-4.132
>
> I am starting to pull my peptide from 1nm above the upper leaf headgroup. I 
> am using POPC lipids and distance between 2 adjacent headgroups seem to be 
> around 4.2 nm.
>
> I want the peptide to be pulled into the bilayer till the lower leaf lipid 
> headgroups, but the peptide is being pulled only till middle of the 
> hydrophobic core of the bilayer.
>
> Please can I know what might be the problem ?
>

Either you're (1) not pulling for sufficient time, (2) not pulling hard enough,
or (3) the physical properties of the system don't allow for such a position.

For (2), using a harmonic potential to try to force a peptide into a membrane is
probably not a great idea.  A constraint force is probably better.  For (3),
what does "POSRES_LIPID" refer to?  Are you keeping the lipids too rigid by
doing so?

>
> While viewing the conf.*gro file outputed  from the traj. (after extracting 
> the frames), i found few lipid molecules to be broken. Please can I know if 
> there is a way to avoid these broken structures??? Is there a possibility 
> that I am not able to pull the peptide into the lower leaf head group due to 
> these broken lipid structures?
>
>

Please become comfortable with the concept of periodic boundary conditions.

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

-Justin

>
>
> Any suggestions will be helpful.
>
>
> Kind regards,
> chetan.
>
> 
> 
> Forschungszentrum Juelich GmbH
> 52425 Juelich
> Sitz der Gesellschaft: Juelich
> Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
> Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher
> Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender),
> Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
> Prof. Dr. Sebastian M. Schmidt
> 
> 

--


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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