Re: [gmx-users] Protein is having non-integral charge

[Mark Abraham]

On 7/04/2010 4:03 PM, sonali dhindwal wrote:

Hello All
I am using gromacs for simulating my protein I got after homology modelling.
While doing this when I get toplogy file by using
0: GROMOS96 43a1 force field
topology file I am getting has most of the residues having non-integral
charge.
Can someone help in this.
As far as I searched for this, it is written that the charge should be
integer.


Yes, each residue's charge needs to be an integer, and thus the whole 
charge also. Something's badly broken, either with what pdb2gmx is doing 
with your homology model, or how you're choosing termini. Look at the 
running counter of total charge on the right hand side of the listing in 
the [atoms] section of your .top file to see where things are going wrong.


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/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/mailing_lists/users.php

Re: [gmx-users] link gromacs i7

[XAvier Periole]

We have been using gromacs-4.0.7 on I7 with up to 8 CPUs. The
scaling is pretty good.
Note that upgrading to openmpi-1.4.1 was necessary to be able
to scale to up to 8 CPUs, if not the jobs where hanging ...
Since you have it already, I do not see where the problem can
come from. Are you sure you are using openmpi-1.4.1?

On Apr 7, 2010, at 12:50 AM, Mark Abraham wrote:


On 7/04/2010 5:32 AM, Maurício Menegatti Rigo wrote:


We are using an i7 920 processor to run Gromacs-4.0.7 with
openmpi-1.4.1. The simulations run well using 4 threads (using  
"mpirun

-np 4 mdrun...") but the performance is worse when we use 6 or 8
threads.


Sure. You have four physical cores. If you're trying to get more  
across a network, unless it is Infiniband you will take a big  
performance hit. Intel's hyperthreading may work (it did 5 years ago  
on different technology), but only if it is turned on, the MPI  
processes are all on the same piece of processor, and you compile  
with MPI and use mpirun -np x for x=1-8.


Even then, 8 virtual cores might over-saturate cache bandwidth, or  
something. You'll need to provide a lot more information for more  
help there.



Looking for some way to improve our performance we found out
this forum and then started to try use threads without openmpi. We
compiled gromacs again and used the command line as described here
("mdrun -nt 8..."), but the following error appears:

--
Program mdrun, VERSION 4.0.7
Source code file: mdrun.c, line: 410

Fatal error:
GROMACS compiled without threads support - can only use one thread
--

But in gromacs-4.0.7 threads are not supposed to be ON by default?


No post to this list has implied that threads work, because they  
will not before GROMACS 4.1. The fact that the installation guides  
on the website don't suggest using threads would also have guided  
you here.


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/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/mailing_lists/users.php


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php

RE: [gmx-users] link gromacs i7

[Berk Hess]

Hi,

I am using openmpi 1.2.8 and it works fine.
You get 15% performance increase when going from 4 to 8 processes.
Note that with 4 processes you have to use:
mpirun -np 4 taskset 0xf mdrun ...
to avoid two processes running on the same physical core.

The only problem I can think of is that your system is so small
that it will anyhow not scale to more than 4 processes.

Berk

> From: x.peri...@rug.nl
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] link gromacs i7
> Date: Wed, 7 Apr 2010 10:10:26 +0200
> 
> 
> We have been using gromacs-4.0.7 on I7 with up to 8 CPUs. The
> scaling is pretty good.
> Note that upgrading to openmpi-1.4.1 was necessary to be able
> to scale to up to 8 CPUs, if not the jobs where hanging ...
> Since you have it already, I do not see where the problem can
> come from. Are you sure you are using openmpi-1.4.1?
> 
> On Apr 7, 2010, at 12:50 AM, Mark Abraham wrote:
> 
> > On 7/04/2010 5:32 AM, Maurício Menegatti Rigo wrote:
> >>
> >> We are using an i7 920 processor to run Gromacs-4.0.7 with
> >> openmpi-1.4.1. The simulations run well using 4 threads (using  
> >> "mpirun
> >> -np 4 mdrun...") but the performance is worse when we use 6 or 8
> >> threads.
> >
> > Sure. You have four physical cores. If you're trying to get more  
> > across a network, unless it is Infiniband you will take a big  
> > performance hit. Intel's hyperthreading may work (it did 5 years ago  
> > on different technology), but only if it is turned on, the MPI  
> > processes are all on the same piece of processor, and you compile  
> > with MPI and use mpirun -np x for x=1-8.
> >
> > Even then, 8 virtual cores might over-saturate cache bandwidth, or  
> > something. You'll need to provide a lot more information for more  
> > help there.
> >
> >> Looking for some way to improve our performance we found out
> >> this forum and then started to try use threads without openmpi. We
> >> compiled gromacs again and used the command line as described here
> >> ("mdrun -nt 8..."), but the following error appears:
> >>
> >> --
> >> Program mdrun, VERSION 4.0.7
> >> Source code file: mdrun.c, line: 410
> >>
> >> Fatal error:
> >> GROMACS compiled without threads support - can only use one thread
> >> --
> >>
> >> But in gromacs-4.0.7 threads are not supposed to be ON by default?
> >
> > No post to this list has implied that threads work, because they  
> > will not before GROMACS 4.1. The fact that the installation guides  
> > on the website don't suggest using threads would also have guided  
> > you here.
> >
> > 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/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/mailing_lists/users.php
> 
> -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
  
_
Express yourself instantly with MSN Messenger! Download today it's FREE!
http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php

RE: [gmx-users] Re: loab imbalance

[Berk Hess]

> From: zhao0...@ntu.edu.sg
> To: gmx-users@gromacs.org
> Date: Tue, 6 Apr 2010 20:45:37 +0800
> Subject: [gmx-users] Re: loab imbalance
> 
> 
> > > > On 6/04/2010 5:39 PM, lina wrote:
> > > > > Hi everyone,
> > > > >
> > > > > Here is the result of the mdrun which was performed on 16cpus. I am 
> > > > > not
> > > > > clear about it, was it due to using MPI reason? or some other reasons.
> > > > >
> > > > > Writing final coordinates.
> > > > >
> > > > >   Average load imbalance: 1500.0 %
> > > > >   Part of the total run time spent waiting due to load imbalance: 
> > > > > 187.5 %
> > > > >   Steps where the load balancing was limited by -rdd, -rcon and/or 
> > > > > -dds:
> > > > > X 0 % Y 0 %
> > > > >
> > > > > NOTE: 187.5 % performance was lost due to load imbalance
> > > > >in the domain decomposition.
> > > > 
> > > > You ran an inefficient but otherwise valid computation. Check out the 
> > > > manual section on domain decomposition to learn why it was inefficient, 
> > > > and whether you can do better.
> > > > 
> > > > Mark
> > > 
> > > I search the "decomposition" keyword on Gromacs manual, no match found.
> > > Are you positive about that? Thanks any way, but can you make it more
> > > problem-solved-oriented, so I can easily understand.
> > > 
> > > Thanks and regards,
> > > 
> > > lina
> > 
> > This looks strange.
> > You have 1 core doing something and 15 cores doing nothing.
> > Do you only have one small molecule?
> > How many steps was this simulation?
> > 
> > Berk
> 
> I do not think there was only 1 core doing something and other 15 cores
> doing nothing.
> 
> Below is the time-consumed on 8 cpus and 16 cpus. I tried twice to
> compare the results. 
> 
> 8cpus:
>   Parallel run - timing based on wallclock.
> 
>NODE (s)   Real (s)  (%)
>Time:  52292.000  52292.000100.0
>14h31:32
>(Mnbf/s)   (GFlops)   (ns/day)  (hour/ns)
> Performance:523.244 19.720 16.523  1.453
> Finished mdrun on node 0 Tue Apr  6 05:09:47 2010
> 
> 16cpus:
> 
>   Parallel run - timing based on wallclock.
> 
>NODE (s)   Real (s)  (%)
>Time:  96457.000  96457.000100.0
>1d02h47:37
>(Mnbf/s)   (GFlops)   (ns/day)  (hour/ns)
> Performance:283.696 10.701  8.957  2.679
> Finished mdrun on node 0 Mon Apr  5 01:36:18 2010
> 
> Thanks and regards,
> 
> lina

The first time I did not notice that 16 cpus are twice as slow as 8.
Are you really sure you did not mix things up?
The other way around the timings would make perfect sense.
If not, there is a problem with your 16 cpu simulation.

What load imbalance is reported for the 8 cpu run?

Berk

  
_
New Windows 7: Find the right PC for you. Learn more.
http://windows.microsoft.com/shop-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php

[gmx-users] converting parmbsc0 dihedrals to RB function

[Vigneshwar Ramakrishnan]

Dear Users,



I am trying to port the new parmbsc0 forcefield (
http://mmb.pcb.ub.es/PARMBSC0/frcmod.parmbsc0) into gromacs for DNA
simulations.

While unit conversions are sufficient to convert many of the parameters from
AMBER to GROMACS format, dihedral angle conversion does not seem to be
straight forward - the dihedral parameters need to be converted to the
Ryckaert-Bellemans parameters. I went through the GROMACS 4.0 manual,
especially equations 4.61-4.65 to understand the procedure. The procedure
involves comparing the fourier expansion of the IUPAC convention of dihedral
potential (equation 4.65) with the Ryckaert-Bellemans (RB) functional of
dihedral potential (equation 4.62) to get the Cn's of the RB function.
However, I am not able to understand how to account for the phase angles.
(Also to note, the parmbsc0 forcefield contains phase angles other than 0
and 180.)



 Any advice or suggestion will be of great help.



Thank you,

Vignesh

-- 
R.Vigneshwar
Graduate Student,
Dept. of Chemical & Biomolecular Engg,
National University of Singapore,
Singapore

"Strive for Excellence, Never be satisfied with the second Best!!"

I arise in the morning torn between a desire to improve the world and a
desire to enjoy the world. This makes it hard to plan the day. (E.B. White)
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php

[gmx-users] Re: converting parmbsc0 dihedrals to RB function

[Alan]

I strongly advice you to contact Eric Sorin from ffAMBER project as he's
onto that and you maybe can add to his efforts.

http://ffamber.cnsm.csulb.edu/

Alan


On Wed, Apr 7, 2010 at 11:00,  wrote:

> I am trying to port the new parmbsc0 forcefield (
> http://mmb.pcb.ub.es/PARMBSC0/frcmod.parmbsc0) into gromacs for DNA
> simulations.
>
> While unit conversions are sufficient to convert many of the parameters
> from
> AMBER to GROMACS format, dihedral angle conversion does not seem to be
> straight forward - the dihedral parameters need to be converted to the
> Ryckaert-Bellemans parameters. I went through the GROMACS 4.0 manual,
> especially equations 4.61-4.65 to understand the procedure. The procedure
> involves comparing the fourier expansion of the IUPAC convention of
> dihedral
> potential (equation 4.65) with the Ryckaert-Bellemans (RB) functional of
> dihedral potential (equation 4.62) to get the Cn's of the RB function.
> However, I am not able to understand how to account for the phase angles.
> (Also to note, the parmbsc0 forcefield contains phase angles other than 0
> and 180.)
>



-- 
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php

[gmx-users] Re: loab imbalance

[lina]

> The first time I did not notice that 16 cpus are twice as slow as 8.
> Are you really sure you did not mix things up?
> The other way around the timings would make perfect sense.
> If not, there is a problem with your 16 cpu simulation.
> 
> What load imbalance is reported for the 8 cpu run?
> 
> Berk
> 

Sorry, recently so sleepy, so I mixed up with the 8cpus and 16 cpus in
the last email. no doubt that the 16 cpus fast. Seems 8 cpus no
problems. 
 
D O M A I N   D E C O M P O S I T I O N   S T A T I S T I C S

 av. #atoms communicated per step for force:  2 x 70598.6
 av. #atoms communicated per step for LINCS:  2 x 952.6

 Average load imbalance: 1500.0 %
 Part of the total run time spent waiting due to load imbalance: 187.5 %
 Steps where the load balancing was limited by -rdd, -rcon and/or -dds:
X 0 % Y 
0 %

NOTE: 187.5 % performance was lost due to load imbalance
  in the domain decomposition.


 R E A L   C Y C L E   A N D   T I M E   A C C O U N T I N G

 Computing: Nodes Number G-CyclesSeconds %
---
 Domain decomp.16100   121878.35036533.7 4.4
 Comm. coord.  16501   247646.11474233.2 8.9
 Neighbor search   16101  1002091.741   300382.235.9
 Force 16501   919401.942   275595.532.9
 Wait + Comm. F16501   299888.01789893.010.7
 Write traj.   16   2001  249.523   74.8 0.0
 Update1650120258.672 6072.6 0.7
 Constraints   16501   105721.49231690.6 3.8
 Comm. energies1650151653.35315483.4 1.9
 Rest  16   22395.593 6713.2 0.8
---
 Total 16 2791184.797   836672.0   100.0
---

Parallel run - timing based on wallclock.

   NODE (s)   Real (s)  (%)
   Time:  52292.000  52292.000100.0
   14h31:32
   (Mnbf/s)   (GFlops)   (ns/day)  (hour/ns)
Performance:523.244 19.720 16.523  1.453
Finished mdrun on node 0 Tue Apr  6 05:09:47 2010
\\\(below is
8cpu's md.log)

D O M A I N   D E C O M P O S I T I O N   S T A T I S T I C S

 av. #atoms communicated per step for force:  2 x 46783.6
 av. #atoms communicated per step for LINCS:  2 x 664.8

 Average load imbalance: 9.8 %
 Part of the total run time spent waiting due to load imbalance: 3.5 %


 R E A L   C Y C L E   A N D   T I M E   A C C O U N T I N G

 Computing: Nodes Number G-CyclesSeconds %
---
 Domain decomp. 810069839.47420934.6 2.7
 Comm. coord.   8501   162704.62548771.3 6.3
 Neighbor search8101   982919.098   294633.338.2
 Force  8501   917463.617   275012.835.6
 Wait + Comm. F 8501   273548.44981997.110.6
 Update 850120465.372 6134.6 0.8
 Constraints850196414.22228900.5 3.7
 Comm. energies 850128884.158 8658.1 1.1
 Rest   89223372036.855 2764736802.2
358286.2
---
 Total  8 2574303.046   771656.0   100.0
---

Parallel run - timing based on wallclock.

   NODE (s)   Real (s)  (%)
   Time:  96457.000  96457.000100.0
   1d02h47:37
   (Mnbf/s)   (GFlops)   (ns/day)  (hour/ns)
Performance:283.696 10.701  8.957  2.679
Finished mdrun on node 0 Mon Apr  5 01:36:18 2010

Thanks and regards,

lina

--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php

[gmx-users] Regarding inflategro.pl

[Jignesh Patel]

Dear Justin,

When I used inflategro.pl, it removed original water molecules of DPPC128
membrane.

After that i added water using genbox.

Is it correct method to follow?

Thanking you in anticipation.

-- 
Best Wishes,
Jignesh Patel
Pharmacoinformatics,
NIPER
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php

Re: [gmx-users] Regarding inflategro.pl

[Justin A. Lemkul]

Jignesh Patel wrote:

Dear Justin,

When I used inflategro.pl , it removed original 
water molecules of DPPC128 membrane.


After that i added water using genbox.

Is it correct method to follow?



Yes.

-Justin


Thanking you in anticipation.

--
Best Wishes,
Jignesh Patel
Pharmacoinformatics,
NIPER



--


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/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/mailing_lists/users.php

[gmx-users] Re: Query regarding Gromacs

[Justin A. Lemkul]

Please keep all Gromacs-related correspondence on the gmx-users list.  I am not 
a private tutor or help service, and you stand a much better chance of getting 
an answer by contacting the community.


I have never worked with a system like yours, so I don't know why you'd assume I 
have such a protocol.  In general, you should principally be concerned with 
deriving proper parameters for your copper ion and quinone:


http://www.gromacs.org/Documentation/How-tos/Parameterization

Please realize that parameterization is a very advanced topic (especially note 
the "Exotic Species" heading in the above page).


I have no idea what you mean by "the heteroatoms are getting converted to atoms" 
- is there some issue with PDB nomenclature (HETATM/ATOM)?  If so, there is no 
problem.


-Justin

charanya wrote:

Dear Mr. Justin A. Lemkul,

I am working on copper dependent amine oxidases which have quinone and copper 
cofactors. These are essential for the proper functioning of the enzyme.When I tried 
to minimize the complex, the heteroatoms are getting converted to atoms. I request you 
to kindly provide me with a protocol as to how to minimize these kind of proteins.


Thank you for your time and consideration.

Regards,
Charanya Muralidharan
Dept of Biochemistry, cell biology & Bioinformatics
Sankara Nethralaya
18 College Road
Chennai . 600 006
Phone: 044-28271616 Fax: 044-28254180
Please visit our web site:  www.supportsankaranethralaya.org

FOR CORRECTION OF REFRACTIVE ERRORS WITH EXCIMER LASER PLEASE CALL: 0 93821
47796 & 0 93801 07258 OR E MAIL:la...@snmail.org

Confidentiality Notice: This transmittal is a confidential communication. If you are 
not the intended recipient, you are hereby notified that you have received this 
transmittal in error and that any review, dissemination, distribution or copying of 
this transmittal is strictly prohibited. If you have received this communication in 
error, please notify this office immediately by reply and immediately delete this 
message and all of its attachments, if any.





--


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/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/mailing_lists/users.php

[gmx-users] position_restraint anfd full Dynamics and berendsen Nose hoover Thermostat

[shahid nayeem]

Dear users
Please let me know some basic question. I am sorry if I am asking a silly
question.
a) While simulating a protein thermal unfolding at high temperature say 500K
should I run position restraint dynamics at 500k or at 298K. I am doing
100ps position restraint dynamics at 500k. Am I right in doing so.
b) While using Berendsen thermostat, how to select a value of tau_t and how
does it affects simulation output. The same question for NoseHoover
thermostat.
c) After completing the 100ns simulation when I view the .xtc file in VMD I
find that  alpha helix of the protein is unfolded in very first frame
collected at 10ps interval and reduced by trjconv  at 50ps interval. Is it
possible. If not then where I am wrong.
I did Steepest descent minimization, then 100ps position restraint Dynamics
at 500K and then 100ns full dynamics at 500k.
msnayeem
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php

[gmx-users] coarse-grained model of POPC in Martini coarse-grained force field?

[xi zhao]

I'd like to run simulations with coarse grained model lipid bilayer.
 I can not  find the force field for coarse grain POPC lipid or equilibrated 
bilayer coordinates in Martini website. Please help me! 
thank you!





  -- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php

Re: [gmx-users] converting parmbsc0 dihedrals to RB function

[Mark Abraham]

On 7/04/2010 7:44 PM, Vigneshwar Ramakrishnan wrote:

Dear Users,

I am trying to port the new parmbsc0 forcefield
(http://mmb.pcb.ub.es/PARMBSC0/frcmod.parmbsc0) into gromacs for DNA
simulations.

While unit conversions are sufficient to convert many of the parameters
from AMBER to GROMACS format, dihedral angle conversion does not seem to
be straight forward - the dihedral parameters need to be converted to
the Ryckaert-Bellemans parameters.


Why? GROMACS can probably do the non-RB form - IIRC you can implement a 
sum of multiple instances of 4.61 with different n.



I went through the GROMACS 4.0
manual, especially equations 4.61-4.65 to understand the procedure. The
procedure involves comparing the fourier expansion of the IUPAC
convention of dihedral potential (equation 4.65) with the
Ryckaert-Bellemans (RB) functional of dihedral potential (equation 4.62)
to get the Cn's of the RB function. However, I am not able to understand
how to account for the phase angles. (Also to note, the parmbsc0
forcefield contains phase angles other than 0 and 180.)


Elegant conversion formulae require those angles to be convenient...

Mark


  Any advice or suggestion will be of great help.

Thank you,

Vignesh

--
R.Vigneshwar
Graduate Student,
Dept. of Chemical & Biomolecular Engg,
National University of Singapore,
Singapore

"Strive for Excellence, Never be satisfied with the second Best!!"

I arise in the morning torn between a desire to improve the world and a
desire to enjoy the world. This makes it hard to plan the day. (E.B. White)


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php

Re: [gmx-users] coarse-grained model of POPC in Martini coarse-grained force field?

[XAvier Periole]

POPC lipid is defined in the lipid itp file you'll find on the website.

http://md.chem.rug.nl/cgmartini/index.php/forcefield-parameters/56-lipids

POPC coordinate file is indeed not present on the website. However,
transforming a DOPC or DPPC coordinate file to a POPC coordinate
file goes only by modifying the central bead name in the first tail for
DOPC or second tail in DPPC to the one of POPC. Then change the
residue name.
Take a topology of DOPC or DPPC, modify what is needed to make
it be for POPC (basically change the name in it) and then equilibrate
your box ...

It is that easy, isn't it beautiful :))

On Apr 7, 2010, at 2:11 PM, xi zhao wrote:



I'd like to run simulations with coarse grained model lipid bilayer.
 I can not  find the force field for coarse grain POPC lipid or  
equilibrated bilayer coordinates in Martini website. Please help me!

thank you!




 --
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php


-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php

Re: [gmx-users] position_restraint anfd full Dynamics and berendsen Nose hoover Thermostat

[Mark Abraham]

On 7/04/2010 9:08 PM, shahid nayeem wrote:

Dear users
Please let me know some basic question. I am sorry if I am asking a
silly question.
a) While simulating a protein thermal unfolding at high temperature say
500K should I run position restraint dynamics at 500k or at 298K. I am
doing 100ps position restraint dynamics at 500k. Am I right in doing so.


The usual purpose of position restrained MD is to allow the system to 
achieve close to the ensemble desired for the start of the simulation 
without perturbing the initial structure.



b) While using Berendsen thermostat, how to select a value of tau_t and
how does it affects simulation output. The same question for NoseHoover
thermostat.


Start by reading the GROMACS manual sections.


c) After completing the 100ns simulation when I view the .xtc file in
VMD I find that  alpha helix of the protein is unfolded in very first
frame collected at 10ps interval and reduced by trjconv  at 50ps
interval. Is it possible. If not then where I am wrong.
I did Steepest descent minimization, then 100ps position restraint
Dynamics at 500K and then 100ns full dynamics at 500k.


10ps would be very fast for a lengthy helix to unfold, however you've 
deliberately taken your force field out of the zone where it was 
parameterized, so we can't really infer anything about its behaviour. 
You could also have a broken model physics in your .mdp file, but we 
can't know about that.


The real lesson here is not to do a lengthy simulation without looking 
at the early and ongoing results.


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/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/mailing_lists/users.php

[gmx-users] Free Energy Calculations for linkage change

[Sai Kumar Ramadugu]

Dear All,
   I have an disaccharide bound to a C-type lectin. The sequence of
disaccharide is beta-galactose1-4beta-GlcNAc. The 3'OH and 4'OH  of
beta-galactose coordinate to the Ca2+ at the active site. FRET experiments
have shown that if the disaccharide linkage is changed to
beta-galactose1-3beta-GlcNAc then the binding affinity drops to 20 fold. I
have attached both disaccharides in the figure. The left side residue is
galactose and right side residue is N-Acetylgalactoseamine. .
In order to do a free energy perturbation and find the relative free energy
of binding for these two ligands, I have to slowly change the linkage from
beta1-4 to beta1-3. If you look at the models of both disaccharides from the
figure, to convert the beta 1-4 linked disaccharide to beta 1-3 linked
disaccharide, I have to make the the C1 atom of Galactose attached to O4 of
N-Acetylgalactoseamine as H atom and rest of the galactose residue to dummy
atoms. On the other hand I have to grow the residue from H attached to O3 of
N-acetylgalactoseamine to a galactose. The number of atoms involved is 21
atoms. Further the constraints I have is that the sugar should be bound in
right conformation at the active site. So may be I need distance restraints.
Does my approach make any sense? I have seen some papers by others where
they add a fragment or delete a fragment between two ligands. But in my case
the difference is the linkage between two residues.

Thanks for your time in advance.

Regards
Sai Ramadugu
<>-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php

[gmx-users] an energy minimization question, working with H-BONDS

[Miguel Quiliano Meza]

Dear Users.

I am a relative new user of GROMACS and I have some doubts:

I would like to perform a energy minimization (with water and iones) of a
crystal in orden to re-build the H-bonds responsible of the secundary
structure, to achieve this goal I want to restraint the movement of the
protein (aminoacids) and permit the movement of the H-bonds as a product of
add Hydrogens with pdb2gmx.

I think that this task could be define/establish in CONSTRAINS in the ".mdp"
file, I searched in the web and only find this:

 Bonds  constraints:  *none* No constraints except for those defined
explicitly in the topology, i.e. bonds are represented by a harmonic (or
other) potential or a Morse potential (depending on the setting of *morse*)
and angles by a harmonic (or other) potential. *hbonds* Convert the bonds
with H-atoms to constraints. *all-bonds* Convert all bonds to constraints. *
h-angles* Convert all bonds and additionally the angles that involve H-atoms
to bond-constraints. *all-angles* Convert all bonds and angles to
bond-constraints.  What option shoud I use for my objective? My objetive, is
it possible to do? I would be very grateful if someone can help me with some
ideas or advices. thanks in advance Miguel
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php

Re: [gmx-users] an energy minimization question, working with H-BONDS

[Justin A. Lemkul]

Miguel Quiliano Meza wrote:

Dear Users.
 
I am a relative new user of GROMACS and I have some doubts:
 
I would like to perform a energy minimization (with water and iones) of 
a crystal in orden to re-build the H-bonds responsible of the secundary 
structure, to achieve this goal I want to restraint the movement of the 
protein (aminoacids) and permit the movement of the H-bonds as a 
product of add Hydrogens with pdb2gmx.
 
I think that this task could be define/establish in CONSTRAINS in 
the ".mdp" file, I searched in the web and only find this:
 


First, understand that a "constraint" and a "restraint" are very different 
concepts in Gromacs:


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

Thus, the "constraints" keyword is unrelated to what you're looking to do.

Simple energy minimization will seek to relax the structure, forming favorable 
contacts and resolving large forces.  Whether or not this bears any useful 
information about the stability of secondary structure is debatable.  Running 
true MD is a better tool for that purpose, but EM should suffice to form any 
hydrogen bonds that are reasonably close in space.


I don't think it will be meaningful at all to restrain part of the protein and 
hope that hydrogen bonds in the backbone re-orient.  You'd essentially be fixing 
the side chain positions, which will not allow for much re-organization, not 
that I'd expect to see major changes during EM, anyway.


-Justin




  Bonds


constraints:

*none*
No constraints except for those defined explicitly in the
topology, i.e. bonds are represented by a harmonic (or other)
potential or a Morse potential (depending on the setting of
*morse*) and angles by a harmonic (or other) potential. 
*hbonds*
Convert the bonds with H-atoms to constraints. 
*all-bonds*
Convert all bonds to constraints. 
*h-angles*

Convert all bonds and additionally the angles that involve
H-atoms to bond-constraints. 
*all-angles*
Convert all bonds and angles to bond-constraints. 

What option shoud I use for my objective? My objetive, is it possible to 
do? I would be very grateful if someone can help me with some ideas or 
advices.


thanks in advance

Miguel



--


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/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/mailing_lists/users.php

Re: [gmx-users] problem with total energy

[ms]

jampani srinivas ha scritto:
> Dear Berk,
> 
> I am sorry if i am confusing you with my poor description of problem,
> actually I have submitted simulation with two temperature coupling groups (i
> think you already know that from our earlier conversations) and found that
> there is a continuous increase in the total energy of the system. I could
> not observe any blowing in the output file but the system energy is
> continuously increasing, i am using 4fs time step here. Can you please let
> me know if i have to give more details?
> 

Which part of the system is increasing its energy?

m.
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php

[gmx-users] Re: converting parmbsc0 dihedrals to RB function

[Alan]

>From ffamber (in e.g. .../gromacs/top/ffamber99sbbon.itp):

- impropers treated as propers in GROMACS to use correct AMBER analytical
function
- propers treated as RBs in GROMACS to use combine multiple AMBER torsions
per quartet

I followed these instructions while building acpypi (acpypi.googlecode.com/
).

You can study my code and see how the conversion is done (I put the details
inside acpypi.py).

I didn't test acpypi with an amber prmtop/inpcrd input with parmbsc0
parameters, but it would be interesting to see what I would get.

Bear in mind that if parmbsc0 were "simple" to port, then it would have been
done since the first version of ffamber, but I know Eric Sorin is working on
that now.

Alan

On Wed, Apr 7, 2010 at 22:00,  wrote:

> > Dear Users,
> >
> > I am trying to port the new parmbsc0 forcefield
> > (http://mmb.pcb.ub.es/PARMBSC0/frcmod.parmbsc0) into gromacs for DNA
> > simulations.
> >
> > While unit conversions are sufficient to convert many of the parameters
> > from AMBER to GROMACS format, dihedral angle conversion does not seem to
> > be straight forward - the dihedral parameters need to be converted to
> > the Ryckaert-Bellemans parameters.
>
> Why? GROMACS can probably do the non-RB form - IIRC you can implement a
> sum of multiple instances of 4.61 with different n.
>
> > I went through the GROMACS 4.0
> > manual, especially equations 4.61-4.65 to understand the procedure. The
> > procedure involves comparing the fourier expansion of the IUPAC
> > convention of dihedral potential (equation 4.65) with the
> > Ryckaert-Bellemans (RB) functional of dihedral potential (equation 4.62)
> > to get the Cn's of the RB function. However, I am not able to understand
> > how to account for the phase angles. (Also to note, the parmbsc0
> > forcefield contains phase angles other than 0 and 180.)
>
> Elegant conversion formulae require those angles to be convenient...
>
> Mark
>



-- 
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php

[gmx-users] Free Energy Calculations for linkage change in disaccharide

[Sai Kumar Ramadugu]

Dear All,

In my previous email the text in the message was not shown. Thats why I'm
writing this again.
I request to see the attachment  of earlier message. I'm sorry for this!!

   I have an disaccharide bound to a C-type lectin. The sequence of
disaccharide is beta-galactose1-4beta-GlcNAc. The 3'OH and 4'OH  of
beta-galactose coordinate to the Ca2+ at the active site. FRET experiments
have shown that if the disaccharide linkage is changed to
beta-galactose1-3beta-GlcNAc then the binding affinity drops to 20 fold. I
have attached both disaccharides in the figure. The left side residue is
galactose and right side residue is N-Acetylgalactoseamine. .
In order to do a free energy perturbation and find the relative free energy
of binding for these two ligands, I have to slowly change the linkage from
beta1-4 to beta1-3. If you look at the models of both disaccharides from the
figure, to convert the beta 1-4 linked disaccharide to beta 1-3 linked
disaccharide, I have to make the the C1 atom of Galactose attached to O4 of
N-Acetylgalactoseamine as H atom and rest of the galactose residue to dummy
atoms. On the other hand I have to grow the residue from H attached to O3 of
N-acetylgalactoseamine to a galactose. The number of atoms involved is 21
atoms. Further the constraints I have is that the sugar should be bound in
right conformation at the active site. So may be I need distance restraints.
Does my approach make any sense? I have seen some papers by others where
they add a fragment or delete a fragment between two ligands. But in my case
the difference is the linkage between two residues.

Thanks for your time in advance.

Regards
Sai
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php

[gmx-users] Lateral pressure profile in membrane simulations

[Fernando E. Herrera]

Dear users:

I am doing some molecular dynamics simulations of membrane systems and i
would like to ask you if someone know or have a code for the calculation of
the lateral pressure profile  from the data obtained doing  membrane
simulations.
Thank you very much in advance,

Fernando
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php

RE: [gmx-users] Lateral pressure profile in membrane simulations

[Dallas B. Warren]

Isn't that already present in the energy file, .edr, from the run?
Simply use g_energy to extract it.

 

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@pharm.monash.edu.au
+61 3 9903 9167
-
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 Fernando E. Herrera
Sent: Thursday, 8 April 2010 8:45 AM
To: gmx-users@gromacs.org
Subject: [gmx-users] Lateral pressure profile in membrane simulations

 

Dear users:

I am doing some molecular dynamics simulations of membrane systems and i
would like to ask you if someone know or have a code for the calculation
of the lateral pressure profile  from the data obtained doing  membrane
simulations.
Thank you very much in advance,

Fernando
 

-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php

Re: [gmx-users] Potential Tables for user defined potentials

[Justin A. Lemkul]

Justin A. Lemkul wrote:



Gareth Tribello wrote:

Hello again

OK I have posted my notes on user defined potnetials here.  I think 
there pretty exaustive (well they have everything I know about this 
in) and could be used as a how to in this form.  However, I can't work 
out how to post them on the webiste as a how to page.




Great, I'll try to find some time to get a How-To together and post this 
file as an attachment.  I'll report back when that's done so others can 
add to it.


OK, I've got this all wikified now, complete with fancy equations :)

http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials

Hopefully this information will help de-complicate the issue of tabulated 
potentials, and now that the page is set up, everyone can feel free to add and 
modify to their hearts' content.


-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


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php

[gmx-users] Memory corruption on SAS computation of a large (~1000000 frames) file

[Camilo Andrés Jimenez Cruz]

Hi all

I am using gromacs-3.3.99's g_sas_s  in a long trajectory and I get this
error right away. I assume its memory capacity, is there a way (other than
cutting the trj in smaller chunks?)

Select a group: Select a group: *** glibc detected ***
/usr/local/gromacs-3.3.99_20071008/bin/g_sas_s: malloc(): memory corruption:
 0x0a809680 ***
=== Backtrace: =
/lib64/libc.so.6[0x38b8c71d21]
/lib64/libc.so.6(__libc_calloc+0xc3)[0x38b8c72bb3]
/usr/local/gromacs-3.3.99_20071008/bin/g_sas_s[0x4257d5]
/usr/local/gromacs-3.3.99_20071008/bin/g_sas_s[0x40419a]
/usr/local/gromacs-3.3.99_20071008/bin/g_sas_s[0x405b1a]
/usr/local/gromacs-3.3.99_20071008/bin/g_sas_s[0x402de3]
/lib64/libc.so.6(__libc_start_main+0xf4)[0x38b8c1d8b4]
/usr/local/gromacs-3.3.99_20071008/bin/g_sas_s[0x402d19]
=== Memory map: 
0040-00599000 r-xp  08:05 813706
/usr/local/gromacs-3.3.99_20071008/bin/g_sas_s
00799000-007a2000 rwxp 00199000 08:05 813706
/usr/local/gromacs-3.3.99_20071008/bin/g_sas_s
007a2000-007ad000 rwxp 007a2000 00:00 0
0a7dd000-0a84 rwxp 0a7dd000 00:00 0

thanks in advance

-- 
Camilo Andrés Jiménez Cruz
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php

Re: [gmx-users] Memory corruption on SAS computation of a large (~1000000 frames) file

[Mark Abraham]

On 8/04/2010 10:22 AM, Camilo Andrés Jimenez Cruz wrote:

Hi all

I am using gromacs-3.3.99's g_sas_s  in a long trajectory and I get this
error right away. I assume its memory capacity, is there a way (other
than cutting the trj in smaller chunks?)


Use a bigger computer? See g_sas -h for some built-in options to do a 
smaller part of the calculation.


Mark


Select a group: Select a group: *** glibc detected ***
/usr/local/gromacs-3.3.99_20071008/bin/g_sas_s: malloc(): memory corruption:
  0x0a809680 ***
=== Backtrace: =
/lib64/libc.so.6[0x38b8c71d21]
/lib64/libc.so.6(__libc_calloc+0xc3)[0x38b8c72bb3]
/usr/local/gromacs-3.3.99_20071008/bin/g_sas_s[0x4257d5]
/usr/local/gromacs-3.3.99_20071008/bin/g_sas_s[0x40419a]
/usr/local/gromacs-3.3.99_20071008/bin/g_sas_s[0x405b1a]
/usr/local/gromacs-3.3.99_20071008/bin/g_sas_s[0x402de3]
/lib64/libc.so.6(__libc_start_main+0xf4)[0x38b8c1d8b4]
/usr/local/gromacs-3.3.99_20071008/bin/g_sas_s[0x402d19]
=== Memory map: 
0040-00599000 r-xp  08:05 813706
/usr/local/gromacs-3.3.99_20071008/bin/g_sas_s
00799000-007a2000 rwxp 00199000 08:05 813706
/usr/local/gromacs-3.3.99_20071008/bin/g_sas_s
007a2000-007ad000 rwxp 007a2000 00:00 0
0a7dd000-0a84 rwxp 0a7dd000 00:00 0

thanks in advance

--
Camilo Andrés Jiménez Cruz


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php

[gmx-users] header intact

[Sepideh Soltani]

-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php

[gmx-users] Fwd: help

[Sepideh Soltani]

-- Forwarded message --
From: Sepideh Soltani 
Date: Wed, Apr 7, 2010 at 11:21 PM
Subject: help
To: gmx-users-requ...@gromacs.org


Hi all,

I am running with gromacs 4.0.5. I am trying to do gromacs tutorial for
drug-enzyme complex. I did this tutorial step by step but when I used the
grompp step befor the energy minimization
"grompp -f em.mdp -c trp_b4em.gro -p trp.top -o trp_em.tpr"
I found the following error:
---
Program grompp, VERSION 4.0.5
Source code file: toppush.c, line: 947

Fatal error:
Atomtype CB not found
---

then I found this your answer in mailing list :

The PRODRG server generates topologies for the gmx force field (ffgmx;
deprecated!). You most likely want to have a topology compliant with the
Gromos96 force fields (e.g. ffG43a2). For this you need to use the beta
version of the PRODRG server.
and
finally  I used Beta version of the PRODRG and used DRGAPH.GRO instead
of DRGFIN.GRO becase I had another problem:
---
Program grompp, VERSION 4.0.5
Source code file: grompp.c, line: 362

Fatal error:
number of coordinates in coordinate file (trp_b4ion.gro, 14622)
 does not match topology (trp.top, 14612)
---
But now when again I used the grompp step befor the energy
minimization ("grompp -f em.mdp -c trp_b4em.gro -p trp.top -o trp_em.tpr" )
I have this problem:
---
Program grompp, VERSION 4.0.5
Source code file: toppush.c, line: 1006

Fatal error:
moleculetype CU1+ is redefined
---
Now I don't know Is this change correct? If yes, How can I solve this
new problem.
If not How can I solve previous  problem.


Thank you for your help,

Hanna
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php

[gmx-users] Fwd: moleculetype CU1+ is redefined

[Sepideh Soltani]

-- Forwarded message --
From: Sepideh Soltani 
Date: Thu, Apr 8, 2010 at 12:33 AM
Subject: Fwd: moleculetype CU1+ is redefined
To: sepideh.solt...@gmail.com




Begin forwarded message:

*From: *Sepideh Soltani 
*Date: *April 8, 2010 12:33:00 AM EDT
*To: *gmx-us...@gromacs.org
*Subject: **moleculetype CU1+ is redefined*

I am running with gromacs 4.0.5. I am trying to do gromacs tutorial for
drug-enzyme complex. I did this tutorial step by step but when I used the
grompp step befor the energy minimization
"grompp -f em.mdp -c trp_b4em.gro -p trp.top -o trp_em.tpr"
I found the following error:
---
Program grompp, VERSION 4.0.5
Source code file: toppush.c, line: 947

Fatal error:
Atomtype CB not found
---

then I found this your answer in mailing list :

The PRODRG server generates topologies for the gmx force field (ffgmx;
deprecated!). You most likely want to have a topology compliant with the
Gromos96 force fields (e.g. ffG43a2). For this you need to use the beta
version of the PRODRG server.
and
finally  I used Beta version of the PRODRG and used DRGAPH.GRO instead
of DRGFIN.GRO becase I had another problem:
---
Program grompp, VERSION 4.0.5
Source code file: grompp.c, line: 362

Fatal error:
number of coordinates in coordinate file (trp_b4ion.gro, 14622)
 does not match topology (trp.top, 14612)
---
But now when again I used the grompp step befor the energy
minimization ("grompp -f em.mdp -c trp_b4em.gro -p trp.top -o trp_em.tpr" )
I have this problem:
---
Program grompp, VERSION 4.0.5
Source code file: toppush.c, line: 1006

Fatal error:
moleculetype CU1+ is redefined
---
Now I don't know Is this change correct? If yes, How can I solve this
new problem.
If not How can I solve previous  problem.


Thank you for your help,

Hanna
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php

Re: [gmx-users] Memory corruption on SAS computation of a large (~1000000 frames) file

[Camilo Andrés Jimenez Cruz]

Thanks, I found the problem, I was using a wrong index file :P My bad,



On Wed, Apr 7, 2010 at 8:32 PM, Mark Abraham wrote:

> On 8/04/2010 10:22 AM, Camilo Andrés Jimenez Cruz wrote:
>
>> Hi all
>>
>> I am using gromacs-3.3.99's g_sas_s  in a long trajectory and I get this
>> error right away. I assume its memory capacity, is there a way (other
>> than cutting the trj in smaller chunks?)
>>
>
> Use a bigger computer? See g_sas -h for some built-in options to do a
> smaller part of the calculation.
>
> Mark
>
>
>  Select a group: Select a group: *** glibc detected ***
>> /usr/local/gromacs-3.3.99_20071008/bin/g_sas_s: malloc(): memory
>> corruption:
>>  0x0a809680 ***
>> === Backtrace: =
>> /lib64/libc.so.6[0x38b8c71d21]
>> /lib64/libc.so.6(__libc_calloc+0xc3)[0x38b8c72bb3]
>> /usr/local/gromacs-3.3.99_20071008/bin/g_sas_s[0x4257d5]
>> /usr/local/gromacs-3.3.99_20071008/bin/g_sas_s[0x40419a]
>> /usr/local/gromacs-3.3.99_20071008/bin/g_sas_s[0x405b1a]
>> /usr/local/gromacs-3.3.99_20071008/bin/g_sas_s[0x402de3]
>> /lib64/libc.so.6(__libc_start_main+0xf4)[0x38b8c1d8b4]
>> /usr/local/gromacs-3.3.99_20071008/bin/g_sas_s[0x402d19]
>> === Memory map: 
>> 0040-00599000 r-xp  08:05 813706
>> /usr/local/gromacs-3.3.99_20071008/bin/g_sas_s
>> 00799000-007a2000 rwxp 00199000 08:05 813706
>> /usr/local/gromacs-3.3.99_20071008/bin/g_sas_s
>> 007a2000-007ad000 rwxp 007a2000 00:00 0
>> 0a7dd000-0a84 rwxp 0a7dd000 00:00 0
>>
>> thanks in advance
>>
>> --
>> Camilo Andrés Jiménez Cruz
>>
>>  --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
>



-- 
Camilo Andrés Jiménez Cruz
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php

Re: [gmx-users] Fwd: help

[Mark Abraham]

On 8/04/2010 2:22 PM, Sepideh Soltani wrote:

Please send one email, not three. If you learn how to use your tools 
properly, you make a much better impression of being someone worth 
someone else's time to help.



-- Forwarded message --
From: *Sepideh Soltani* mailto:sepideh.solt...@gmail.com>>
Date: Wed, Apr 7, 2010 at 11:21 PM
Subject: help
To: gmx-users-requ...@gromacs.org 


Hi all,

I am running with gromacs 4.0.5. I am trying to do gromacs tutorial for
drug-enzyme complex. I did this tutorial step by step but when I used
the grompp step befor the energy minimization
"grompp -f em.mdp -c trp_b4em.gro -p trp.top -o trp_em.tpr"
I found the following error:
---
Program grompp, VERSION 4.0.5
Source code file: toppush.c, line: 947

Fatal error:
Atomtype CB not found
---


Atom types are defined in the ffxxx.itp files that are #included at the 
start of the .top file. Your .top and .gro no longer match, probably 
because you've broken the format of the .top file. Follow the example in 
chapter 5 of the manual, and read the latter parts of that chapter 
thoroughly.



then I found this your answer in mailing list :


Please provide a URL. We can't tell what's a quote and what's your text 
in the stuff below.


If you're using a metal ion, be prepared for problems. See 
http://www.gromacs.org/Documentation/How-tos/Parameterization


Mark


The PRODRG server generates topologies for the gmx force field (ffgmx;
deprecated!). You most likely want to have a topology compliant with the
Gromos96 force fields (e.g. ffG43a2). For this you need to use the beta
version of the PRODRG server.
and
finally  I used Beta version of the PRODRG and used DRGAPH.GRO instead
of DRGFIN.GRO becase I had another problem:
---
Program grompp, VERSION 4.0.5
Source code file: grompp.c, line: 362

Fatal error:
number of coordinates in coordinate file (trp_b4ion.gro, 14622)
  does not match topology (trp.top, 14612)
---
But now when again I used the grompp step befor the energy
minimization ("grompp -f em.mdp -c trp_b4em.gro -p trp.top -o
trp_em.tpr" ) I have this problem:
---
Program grompp, VERSION 4.0.5
Source code file: toppush.c, line: 1006

Fatal error:
moleculetype CU1+ is redefined
---
Now I don't know Is this change correct? If yes, How can I solve this
new problem.
If not How can I solve previous  problem.


Thank you for your help,

Hanna


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php

[gmx-users] energy minimization in charged systems

[Ravi Bhadauria]

Hi all,

I am trying to simulate a electroosmotic flow in a nanochannel. System
consists of water + (Cl-) ions in a channel confined of silicon <111> walls.
I start with taking water as only solvent, equilibrating the system for
about 12-15 ps (gmxcheck runs clean), and then use genion to insert (Cl-)
ions. Walls are charged appropriately to maintain electro-neutrality in the
system. The problem is with Energy minimization after inserting ions using
steep algorithm (haven't turned on the electric field yet). I am getting an
error like this:

t = 0.038 ps: Water molecule starting at atom 2569 can not be settled.
Check for bad contacts and/or reduce the timestep.
Wrote pdb files with previous and current coordinates

and

Steepest Descents converged to machine precision in 88 steps,
but did not reach the requested Fmax < 1000.
Potential Energy  =  1.75456106043895e+06
Maximum force =  1.07111309902475e+11 on atom 4898
Norm of force =  1.48772609239112e+09

If it were only couple of such molecules, I could have removed them easily
from the gro file. The problem is twofold, there are around 10 molecules
which give this error message, plus even after removal of these molecules,
energy minimization results in the same error on different sets of
molecules. I have tried a number of ways to tackle this including tuning the
time step. Is there any way to avoid this? Any help would be appreciated.

Thanks in advance.

-- 
Ravi Bhadauria
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php

RE: [gmx-users] energy minimization in charged systems

[Dallas B. Warren]

What are the atoms that are causing the problems actually doing, where are they 
located etc?

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@pharm.monash.edu.au
+61 3 9903 9167
-
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 Ravi Bhadauria
Sent: Thursday, 8 April 2010 3:11 PM
To: gmx-users@gromacs.org
Subject: [gmx-users] energy minimization in charged systems

Hi all,

I am trying to simulate a electroosmotic flow in a nanochannel. System consists 
of water + (Cl-) ions in a channel confined of silicon <111> walls. I start 
with taking water as only solvent, equilibrating the system for about 12-15 ps 
(gmxcheck runs clean), and then use genion to insert (Cl-) ions. Walls are 
charged appropriately to maintain electro-neutrality in the system. The problem 
is with Energy minimization after inserting ions using steep algorithm (haven't 
turned on the electric field yet). I am getting an error like this:

t = 0.038 ps: Water molecule starting at atom 2569 can not be settled.
Check for bad contacts and/or reduce the timestep.
Wrote pdb files with previous and current coordinates

and

Steepest Descents converged to machine precision in 88 steps,
but did not reach the requested Fmax < 1000.
Potential Energy  =  1.75456106043895e+06
Maximum force =  1.07111309902475e+11 on atom 4898
Norm of force =  1.48772609239112e+09

If it were only couple of such molecules, I could have removed them easily from 
the gro file. The problem is twofold, there are around 10 molecules which give 
this error message, plus even after removal of these molecules, energy 
minimization results in the same error on different sets of molecules. I have 
tried a number of ways to tackle this including tuning the time step. Is there 
any way to avoid this? Any help would be appreciated.

Thanks in advance.

-- 
Ravi Bhadauria
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php

[gmx-users] Simulating a metal slab

[radhika jaswal]

Hii Everybody...



I want to simulate a Titanium Oxide slab of approx. 8-9 molecules in
length and 4-5 molecules wide just as to mimic a rigid metal slab for
further interaction studies. Can gromacs library support this and how I
can do that...

All suggestions are welcome.



Thanks 



Radhika



Send free SMS to your Friends on Mobile from your Yahoo! Messenger. Download 
Now! http://messenger.yahoo.com/download.php-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php

Re: [gmx-users] Simulating a metal slab

[Mark Abraham]

On 8/04/2010 3:47 PM, radhika jaswal wrote:

Hii Everybody...

I want to simulate a Titanium Oxide slab of approx. 8-9 molecules in
length and 4-5 molecules wide just as to mimic a rigid metal slab for
further interaction studies. Can gromacs library support this and how I
can do that...


Yes, in principle. You will need a force field that supports such 
interactions, and GROMACS does not come with any. Your first place to 
look should be in the published literature for other simulations of such 
materials and such slabs. Don't assume GROMACS is the best tool for the 
task.


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/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/mailing_lists/users.php

Re: [gmx-users] position_restraint anfd full Dynamics and berendsen Nose hoover Thermostat

[shahid nayeem]

Please see the following pr.mdp and full.mdp
pr.mdp


cpp = /usr/bin/cpp

define = -DPOSRES

constraints = all-bonds

integrator = md

dt = 0.002 ; ps !

nsteps = 5 ; total 100 ps.

nstcomm = 1

nstxout = 500

nstvout = 1000

nstfout = 0

nstlog = 10

nstenergy = 10

nstlist = 10

ns_type = grid

rlist = 1.0

rcoulomb = 1.0

rvdw = 1.0

; Berendsen temperature coupling is on in two groups

Tcoupl = berendsen

tc-grps = ProteinNon-protein

tau_t = 0.1  0.1

ref_t = 500 500

; Energy monitoring

energygrps = Protein Non-protein

; Pressure coupling is not on

Pcoupl = no

tau_p = 0.5

compressibility = 4.5e-5

ref_p = 1.0

; Generate velocites is on at 500 K.

gen_vel = yes

gen_temp = 500.0

gen_seed = 173529

full.mdp

cpp = /usr/bin/cpp

constraints = all-bonds

integrator = md

dt = 0.002 ; ps !

nsteps = 5000 ; total 10 ps.

nstcomm = 1

nstxout = 5000

nstvout = 4

nstfout = 0

nstlog = 100

nstenergy = 100

nstlist = 10

ns_type = grid

rlist = 1.0

rcoulomb = 1.0

rvdw = 1.0

; Berendsen temperature coupling is on in two groups

Tcoupl = berendsen

tc-grps = Protein   Non-protein

tau_t = 0.10.1

ref_t = 500 500

; Energy monitoring

energygrps = Protein Non-protein

; Isotropic pressure coupling is now on

Pcoupl = berendsen

Pcoupltype = isotropic

tau_p = 0.5

compressibility = 4.5e-5

ref_p = 1.0

; Generate velocites is off at 500 K.

gen_vel = no

gen_temp = 500.0

gen_seed = 173529

Please tell me why protein shows unfolding in very first frame.

msnayeem







On 4/7/10, Mark Abraham  wrote:
>
> On 7/04/2010 9:08 PM, shahid nayeem wrote:
>
>> Dear users
>> Please let me know some basic question. I am sorry if I am asking a
>> silly question.
>> a) While simulating a protein thermal unfolding at high temperature say
>> 500K should I run position restraint dynamics at 500k or at 298K. I am
>> doing 100ps position restraint dynamics at 500k. Am I right in doing so.
>>
>
> The usual purpose of position restrained MD is to allow the system to
> achieve close to the ensemble desired for the start of the simulation
> without perturbing the initial structure.
>
> b) While using Berendsen thermostat, how to select a value of tau_t and
>> how does it affects simulation output. The same question for NoseHoover
>> thermostat.
>>
>
> Start by reading the GROMACS manual sections.
>
> c) After completing the 100ns simulation when I view the .xtc file in
>> VMD I find that  alpha helix of the protein is unfolded in very first
>> frame collected at 10ps interval and reduced by trjconv  at 50ps
>> interval. Is it possible. If not then where I am wrong.
>> I did Steepest descent minimization, then 100ps position restraint
>> Dynamics at 500K and then 100ns full dynamics at 500k.
>>
>
> 10ps would be very fast for a lengthy helix to unfold, however you've
> deliberately taken your force field out of the zone where it was
> parameterized, so we can't really infer anything about its behaviour. You
> could also have a broken model physics in your .mdp file, but we can't know
> about that.
>
> The real lesson here is not to do a lengthy simulation without looking at
> the early and ongoing results.
>
> 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/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/mailing_lists/users.php
>
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php

[gmx-users] Re:Re: g_nmeig_d error:cannot allocate region

[sarbani chattopadhyay]

 Hi,
I had checked and found that gromacs has been compiled in 64 bit mode. However 
still I am getting this error with "g_nmeig_d " command which says
g_nmeig_d(1892) malloc: *** mmap(size=18446744072353271808) failed (error 
code=12)
*** error: can't allocate region


 I am running this on a 8 node machine,each with 2GB of RAM ( g_nmeig_d runs on 
a single node).

Is it required to increase the RAM of 1 node to get rid of this error?
Any suggestion will be very helpful.
Thanking You,
Sarbani



On Tue, 02 Mar 2010 20:01:51 +0530 wrote
>
>
>
Hi,
>

>
The allocation that causes the error should allocate about 3 GB.
>
My guess is that you compiled Gromacs in 32bit mode, whereas 64bit mode
>
is required for allocation of more than 2 GB.
>

>
Berk
>

>
Date: Tue, 2 Mar 2010 13:35:58 +
>
To: gmx-users@gromacs.org
>
From: sarbani_...@rediffmail.com
>
Subject: [gmx-users] g_nmeig_d error: can't allocate region
>

>
Hi,
>

>
I am trying to do normal mode analysis on a protein having 6398 atoms in vaccum.

I tried to energy minimize the structure using steepest descent, followed by 
"l-bfgs"
minimization. the .mdp file I used is

define = -DFLEXIBLE

constraints = none
integrator = l-bfgs
tinit = 0
nsteps = 15000
nbfgscorr = 50
emtol = .001
emstep = 0.1
gen_vel = yes
gen-temp = 300
nstcomm = 1
; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist = 0
; ns algorithm (simple or grid)
ns-type = simple
; Periodic boundary conditions: xyz (default), no (vacuum)
or full (infinite systems only)
pbc = no
rlist = 0
domain-decomposition = no
; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype = Cut-Off
rcoulomb-switch = 0
rcoulomb = 0
; Dielectric constant (DC) for cut-off or DC of reaction field
epsilon-r = 1
; Method for doing Van der Waals
vdw-type = Cut-off
; cut-off lengths
rvdw-switch = 0
rvdw = 0

>
after running the 15000 steps the Fmax was:>
Low-Memory BFGS Minimizer converged to Fmax < 0.001 in 10197 steps

Potential Energy = -8.26391832320506e+04

Maximum force = 9.37558560558845e-04 on atom 4562

Norm of force = 2.24887722104890e-04

Again the "l-bfgs" minimization was run using the same .mdp file( with emtol =
0.01)>
the output was'
>

>
Low-Memory BFGS Minimizer converged to Fmax < 1e-06 in 4143 steps
>

>
Potential Energy = -8.26391832324998e+04
>

>
Maximum force = 9.67927896882578e-07 on atom 3271
>

>
Norm of force = 1.70637151528245e-07
>

>

>

>

>

>

>

>
After this I prepared the "nm.mdp " file for NMA, where I used exactly the same 
parameters
>

>
as the ones used in lbfgs energy minimization( with integrator = nm)
>

>

>

>
the commands that were used were:
>

>
grompp_d -f new_nm.mdp -t new_lbfgs_2.trr -c new_lbfgs_2.gro -o new_nm.tpr 
-zero -p
>

>
../topol.top
>

>

>

>
nohup mdrun_d -v -s new_nm.tpr -deffnm new_nm -mtx new_nm.mtx &
>

>

>

>

>

>
"nohup.out" had the following message:
>

>
Non-cutoff electrostatics used, forcing full Hessian format.Allocating Hessian
>

>
memory...starting normal mode calculation 'Protein'6398 steps.Maximum force: 
9.67928e-07
>

>

>

>

>

>
The run ended successfully:
>

>

>

>
Then i used the command
>

>
g_nmeig_d -f new_nm.mtx -s new_nm.tpr -ol eigenvalue.xvg -v eigenvector.trr
>

>

>

>
I get the following error:
>

>
Reading file new_nm.tpr, VERSION 4.0.7 (double precision)
>

>
Reading file new_nm.tpr, VERSION 4.0.7 (double precision)
>

>
Reading double precision matrix generated by Gromacs VERSION 4.0.7
>

>
Full matrix storage format, nrow=19194, ncols=19194
>

>

>

>
Diagonalizing to find vectors 1 through 50...
>

>
g_nmeig_d(1892) malloc: *** mmap(size=18446744072353271808) failed (error 
code=12)
>

>
*** error: can't allocate region
>

>
*** set a breakpoint in malloc_error_break to debug
>

>

>

>
I am not being able to understand the problem. the computer has a 16gb memory
>

>

>

>

>

>

>

>
If I use different parameters in the nm.mdp file as
>

>

>

>
rlist = 1.5
>

>
domain-decomposition = no
>

>
; OPTIONS FOR ELECTROSTATICS AND VDW
>

>
; Method for doing electrostatics
>

>
coulombtype = switch
>

>
rcoulomb-switch = 1
>

>
rcoulomb = 1.2
>

>
; Dielectric constant (DC) for cut-off or DC of reaction field
>

>
epsilon-r = 1
>

>
; Method for doing Van der Waals
>

>
vdw-type = switch
>

>
; cut-off lengths
>

>
rvdw-switch = 1
>

>
rvdw = 1.2
>

>

>

>

>

>
then i get the message :Maximum force: 3.14171e+03
>

>
Maximum force probably not small enough to ensure that you are in an
>

>
energy well. Be aware that negative eigenvalues may occur when the
>

>
resulting matrix is diagonalized.
>

>

>

>

>

>
I am sorry to post such a lengthy query, but I have no clue about the root of 
the problem.
>

>
Any suggestion will be of great help.
>

>
Thanks in advance,
>

>
Sarbani. -- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)

Re: [gmx-users] position_restraint anfd full Dynamics and berendsen Nose hoover Thermostat

[Mark Abraham]

On 8/04/2010 3:57 PM, shahid nayeem wrote:

Please see the following pr.mdp and full.mdp
pr.mdp


You're using plain cut-off electrostatics, which was last acceptable in 
about 1958. :-)


Get your system simulating stably at room temperature using a sensible 
electrostatics model before worrying about forcing unfolding at high 
temperatures. Make sure you can walk before you try to run.


Mark


cpp = /usr/bin/cpp

define = -DPOSRES

constraints = all-bonds

integrator = md

dt = 0.002 ; ps !

nsteps = 5 ; total 100 ps.

nstcomm = 1

nstxout = 500

nstvout = 1000

nstfout = 0

nstlog = 10

nstenergy = 10

nstlist = 10

ns_type = grid

rlist = 1.0

rcoulomb = 1.0

rvdw = 1.0

; Berendsen temperature coupling is on in two groups

Tcoupl = berendsen

tc-grps = ProteinNon-protein

tau_t = 0.1  0.1

ref_t = 500 500

; Energy monitoring

energygrps = Protein Non-protein

; Pressure coupling is not on

Pcoupl = no

tau_p = 0.5

compressibility = 4.5e-5

ref_p = 1.0

; Generate velocites is on at 500 K.

gen_vel = yes

gen_temp = 500.0

gen_seed = 173529

full.mdp

cpp = /usr/bin/cpp

constraints = all-bonds

integrator = md

dt = 0.002 ; ps !

nsteps = 5000 ; total 10 ps.

nstcomm = 1

nstxout = 5000

nstvout = 4

nstfout = 0

nstlog = 100

nstenergy = 100

nstlist = 10

ns_type = grid

rlist = 1.0

rcoulomb = 1.0

rvdw = 1.0

; Berendsen temperature coupling is on in two groups

Tcoupl = berendsen

tc-grps = Protein   Non-protein

tau_t = 0.10.1

ref_t = 500 500

; Energy monitoring

energygrps = Protein Non-protein

; Isotropic pressure coupling is now on

Pcoupl = berendsen

Pcoupltype = isotropic

tau_p = 0.5

compressibility = 4.5e-5

ref_p = 1.0

; Generate velocites is off at 500 K.

gen_vel = no

gen_temp = 500.0

gen_seed = 173529

Please tell me why protein shows unfolding in very first frame.

msnayeem



On 4/7/10, *Mark Abraham* mailto:mark.abra...@anu.edu.au>> wrote:

On 7/04/2010 9:08 PM, shahid nayeem wrote:

Dear users
Please let me know some basic question. I am sorry if I am asking a
silly question.
a) While simulating a protein thermal unfolding at high
temperature say
500K should I run position restraint dynamics at 500k or at
298K. I am
doing 100ps position restraint dynamics at 500k. Am I right in
doing so.


The usual purpose of position restrained MD is to allow the system
to achieve close to the ensemble desired for the start of the
simulation without perturbing the initial structure.

b) While using Berendsen thermostat, how to select a value of
tau_t and
how does it affects simulation output. The same question for
NoseHoover
thermostat.


Start by reading the GROMACS manual sections.

c) After completing the 100ns simulation when I view the .xtc
file in
VMD I find that  alpha helix of the protein is unfolded in very
first
frame collected at 10ps interval and reduced by trjconv  at 50ps
interval. Is it possible. If not then where I am wrong.
I did Steepest descent minimization, then 100ps position restraint
Dynamics at 500K and then 100ns full dynamics at 500k.


10ps would be very fast for a lengthy helix to unfold, however
you've deliberately taken your force field out of the zone where it
was parameterized, so we can't really infer anything about its
behaviour. You could also have a broken model physics in your .mdp
file, but we can't know about that.

The real lesson here is not to do a lengthy simulation without
looking at the early and ongoing results.

Mark
--
gmx-users mailing list gmx-users@gromacs.org

http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php



--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php

[gmx-users] energy minimization - infinite force on atom

[Evelyne Deplazes]

Hi gmx-users

I am somehow famliar with gromacs but only used it with coarse grained force
fields (Martini) so far, not with all atom ones. I am now trying to run a
simulation on a membrane protein system (protein embedded in a POPC bilayer
solvated with water) using the gromos force field (Gromacs 4.0.2  ffG53a).
Using gromacs tutorials I managed to create the required input files (.gro,
.top and .itp). I at at the stage of running a energy minimization using
position restraints on the protein and the peptide molecules. I can grompp
the input files

grompp -f min_posre.mdp -p topol.top -c system.gro -o topol.tpr -n index.ndx

with the following input file:

--
-
define  = -DPOSRES -DPOSRES_LIPID
integrator  = steep ; Algorithm (steep = steepest descent
minimization)
emtol   = 100.0 ; Stop minimization when the maximum force <
1000.0 kJ/mol/nm
emstep  = 0.01  ; Energy step size
nsteps  = 5 ; Maximum number of (minimization) steps to
perform

; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
nstlist = 1 ; Frequency to update the neighbor list and
long range forces
ns_type = grid  ; Method to determine neighbor list (simple,
grid)
rlist   = 1.2   ; Cut-off for making neighbor list (short
range forces)
coulombtype = PME   ; Treatment of long range electrostatic
interactions
rcoulomb= 1.2   ; Short-range electrostatic cut-off
rvdw= 1.2   ; Short-range Van der Waals cut-off
pbc = xyz   ; Periodic Boundary Conditions (yes/no)
---

and the following topology file

---
; Include forcefield parameters
#include "ffG53a6_lipid.itp"

; Include chain topologies
#include "protein.itp"

; Include Position restraint file
#ifdef POSRES
#include "posre_protein.itp"
#endif

; Include POPC topology
#include "popc.itp"

#ifdef POSRES_LIPID
#include "lipid_posre.itp"
#endif

; Include water topology
#include "spc.itp"

; Include generic topology for ions
#include "ions.itp"

[ system ]
; Name
mscl protein with POPC bilayer

[ molecules ]
; Compound#mols
Protein 1
POPC242
SOL 32145
CL- 91
NA+ 91
---

When I run the simulation I get the following output after 16 steps of the
minimisation
---
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 100

Double precision normally gives you higher accuracy.

Steepest Descents converged to machine precision in 16 steps,
but did not reach the requested Fmax < 100.
Potential Energy  =  8.0175742e+17
Maximum force =inf on atom 4443
Norm of force =inf
---

It seems there is an infinite force on atom 4443 but I don't really
understand what that means. The confout.gro structure looks ok ie the system
has not "exploded". Should the protein not be restrained? How do I know my
position restraints actually work? I tried increasing the force constant of
the restraints or removing the restraints but still get the same output. I
also tried adding -DFLEXIBLE since I am using the spc model, but still the
same output.

can anyone tell me what that message actually means and what is wrong with
my system?

thanks


-- 
Evelyne Deplazes

PhD student
Theoretical Chemistry group
University of Western Australia
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php

Re: [gmx-users] energy minimization - infinite force on atom

[Mark Abraham]

On 8/04/2010 4:23 PM, Evelyne Deplazes wrote:

Hi gmx-users

I am somehow famliar with gromacs but only used it with coarse grained
force fields (Martini) so far, not with all atom ones. I am now trying
to run a simulation on a membrane protein system (protein embedded in a
POPC bilayer solvated with water) using the gromos force field (Gromacs
4.0.2  ffG53a). Using gromacs tutorials I managed to create the required
input files (.gro, .top and .itp). I at at the stage of running a energy
minimization using position restraints on the protein and the peptide
molecules. I can grompp the input files

grompp -f min_posre.mdp -p topol.top -c system.gro -o topol.tpr -n index.ndx

with the following input file:

--
-
define  = -DPOSRES -DPOSRES_LIPID
integrator  = steep ; Algorithm (steep = steepest descent
minimization)
emtol   = 100.0 ; Stop minimization when the maximum
force < 1000.0 kJ/mol/nm
emstep  = 0.01  ; Energy step size
nsteps  = 5 ; Maximum number of (minimization) steps
to perform

; Parameters describing how to find the neighbors of each atom and how
to calculate the interactions
nstlist = 1 ; Frequency to update the neighbor list
and long range forces
ns_type = grid  ; Method to determine neighbor list
(simple, grid)
rlist   = 1.2   ; Cut-off for making neighbor list
(short range forces)
coulombtype = PME   ; Treatment of long range electrostatic
interactions
rcoulomb= 1.2   ; Short-range electrostatic cut-off
rvdw= 1.2   ; Short-range Van der Waals cut-off
pbc = xyz   ; Periodic Boundary Conditions (yes/no)
---

and the following topology file

---
; Include forcefield parameters
#include "ffG53a6_lipid.itp"

; Include chain topologies
#include "protein.itp"

; Include Position restraint file
#ifdef POSRES
#include "posre_protein.itp"
#endif

; Include POPC topology
#include "popc.itp"

#ifdef POSRES_LIPID
#include "lipid_posre.itp"
#endif

; Include water topology
#include "spc.itp"

; Include generic topology for ions
#include "ions.itp"

[ system ]
; Name
mscl protein with POPC bilayer

[ molecules ]
; Compound#mols
Protein 1
POPC242
SOL 32145
CL- 91
NA+ 91
---

When I run the simulation I get the following output after 16 steps of
the minimisation
---
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 100

Double precision normally gives you higher accuracy.

Steepest Descents converged to machine precision in 16 steps,
but did not reach the requested Fmax < 100.
Potential Energy  =  8.0175742e+17
Maximum force =inf on atom 4443
Norm of force =inf
---

It seems there is an infinite force on atom 4443 but I don't really
understand what that means. The confout.gro structure looks ok ie the
system has not "exploded". Should the protein not be restrained? How do
I know my position restraints actually work? I tried increasing the
force constant of the restraints or removing the restraints but still
get the same output. I also tried adding -DFLEXIBLE since I am using the
spc model, but still the same output.

can anyone tell me what that message actually means and what is wrong
with my system?


A useful diagnostic will be to remove the attempts to use position 
restraints in the "define = " line. If you still get an error like this, 
then your problem (massive positive energy, infinite forces) is almost 
certainly a severe atomic overlap, possibly near atom 4443. If so, get 
out a visualization program and look for water overlapping lipid, or 
something. Position restraints won't help resolve gross errors like that...


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/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/mailing_lists/users.php