date:20110921




Saurav Saha wrote:

Dear Everyone,

I am Saurav B. Saha from India. I am newbie to gromacs. I am interested in using gromacs 
for ligand receptor interaction. But when i started my first step by using pdb2gmx 
-f structure.pdb -water tip3p i am getting fatal error (Fatal error:Atom CD not 
found in residue seq.nr. 7 while adding atom
) and from error report when i checked my pdb file i did not find any REMARK 
465 in my pdb file however, in REMARK 470 i got MISSING ATOM report. I am using 
protein structure which has been elucidated my wet lab. Kindly help.
I dont understand where to begin with.



You need an intact model to start with.  There are no Gromacs tools to 
reconstruct missing atoms (aside from H, which is handled by the .hdb file if 
necessary).  You'll have to use external software to model in the missing atom 
before you can proceed.


-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/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] problem with lipid membrane




Parul tew wrote:

Thanks for the reply Justin,
 


  In theory, that should work.  Please post the entirety of your
.mdp file.

Have you done any prior equilibration, or have you moved straight into
annealing?  I would suggest a restrained NVT before applying NPT or
annealing
when using the restraints.

Yes I did the restrained NVT before but the same problem came, 
morover there was a hole in the upper part of the system with the SOL 
molecules displaced. So then I tried to run the annealing but in this 


I'm having trouble visualizing this.  Is the gap between the lipids and water 
molecules, or somewhere else?


case the SOL molecules were intact but similar problem came with the 
lipid membrane. though, just to check then I tried to equilibration with 
restrained NVT where I restrained the movement of the lipid in all the 
x, y, z axis the problem did not occur.




I suppose this will work, although in principle it should not be necessary. 
Recall, though, that restraints are only a biasing potential and do not prevent 
movement, they simply disfavor it.  If a system is wildly far away from 
equilibrium, typical restraints can be overcome to some extent.


-Justin

 


Here is my mdp file

 --

title   = NVT equilibration for B3-DPPC

define= -DPOSRES -DPOSRES_LIPID ; position restrain the 
protein and lipid


 


; Run parameters

integrator  = md; leap-frog integrator

nsteps= 5   ; 2 * 5 = 100 ps

dt  = 0.002   ; 2 fs

; Output control

nstxout   = 100   ; save coordinates every 0.2 ps

nstvout   = 100   ; save velocities every 0.2 ps

nstenergy   = 100   ; save energies every 0.2 ps

nstlog= 100   ; update log file every 0.2 ps

; Bond parameters

continuation  = no; first dynamics run

constraint_algorithm = lincs  ; holonomic constraints

constraints = all-bonds ; all bonds (even heavy atom-H bonds) 
constrained


lincs_iter  = 1 ; accuracy of LINCS

lincs_order = 4 ; also related to accuracy

; Neighborsearching

ns_type   = grid; search neighboring grid cels

nstlist   = 5 ; 10 fs

rlist   = 1.2   ; short-range neighborlist cutoff (in nm)

rcoulomb= 1.2   ; short-range electrostatic cutoff (in nm)

rvdw= 1.2   ; short-range van der Waals cutoff (in nm)

; Electrostatics

coulombtype = PME   ; Particle Mesh Ewald for long-range electrostatics

pme_order   = 4 ; cubic interpolation

fourierspacing= 0.16; grid spacing for FFT

; Temperature coupling is on

tcoupl= V-rescale ; modified Berendsen thermostat

tc-grps   = Protein DPPC SOL_CL-  ; three coupling groups - more 
accurate


tau_t   = 0.1 0.1   0.1   ; time constant, in ps

ref_t   = 323   323   323   ; reference temperature, one 
for each group, in K


; Pressure coupling is off

pcoupl= no; no pressure coupling in NVT

; Periodic boundary conditions

pbc = xyz ; 3-D PBC

; Dispersion correction

DispCorr= EnerPres  ; account for cut-off vdW scheme

; Velocity generation

gen_vel   = yes   ; assign velocities from Maxwell distribution

gen_temp= 323   ; temperature for Maxwell distribution

gen_seed= -1; generate a random seed

; COM motion removal

; These options remove motion of the protein/bilayer relative to the 
solvent/ions


nstcomm   = 1

comm-mode   = Linear

comm-grps   = Protein_DPPC SOL_CL-

--

This is the topology file:

 --

;Include DPPC chain topology

#include dppc.itp

#ifdef POSRES_LIPID

; Position restraint for each lipid

#include lipid_posre.itp

#endif

　

; Include water topology

#include spc.itp

#ifdef POSRES_WATER

; Position restraint for each water oxygen

[ position_restraints ]

; i funct fcx fcy fcz

1 1 1000 1000 1000

#endif

; Include generic topology for ions

#include ions.itp

　

[ system ]

; Name

protein

128-Lipid DPPC Bilayer

[ molecules ]

; Compound #mols

Protein_A 1

DPPC 121

　

SOL 9867

CL- 14

--

thanks

Parul Tewatia

 



--


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

Re: [gmx-users] Dimer simulation problem




Kavyashree M wrote:

Dear users,

I was trying to simulate a protein dimer covalently bond with
a disulphide bond (230+230 aa long). I used usual protocol
as used for simulation of a monomeric protein, using gromacs-
4.5.3, dodecahedron box, tip4p water model and protein to
box distance of 1 (-d in editconf). In the middle of the simulation
when i checked for minimum image violation there was huge
clashes. I am extremely sorry I have been asking regarding this
many times but in this it is a dimer and I am not sure what mistake
I have done because this happened while simulating another dimer
also though not sever. Hence I seek some guidance from this
community regarding the problem. I attach the graph herewith.
Kindly help. Let me know if I need to give any other information.



Please see my post from yesterday for a more detailed reply to this exact same 
type of question.  I am beginning to suspect there's a problem with g_mindist, 
but I have no solid evidence for that claim, just a hunch.  It looks like your 
protein crosses a periodic boundary and that messes up the calculation.  Please 
center the protein in the box with trjconv -center and re-analyze to see if 
there are any differences.


-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/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Dimer simulation problem

2011-09-21 Thread Kavyashree M

Thanks.

On Wed, Sep 21, 2011 at 5:07 PM, Justin A. Lemkul jalem...@vt.edu wrote:

Kavyashree M wrote:

Dear users,

I was trying to simulate a protein dimer covalently bond with
a disulphide bond (230+230 aa long). I used usual protocol
as used for simulation of a monomeric protein, using gromacs-
4.5.3, dodecahedron box, tip4p water model and protein to
box distance of 1 (-d in editconf). In the middle of the simulation
when i checked for minimum image violation there was huge
clashes. I am extremely sorry I have been asking regarding this
many times but in this it is a dimer and I am not sure what mistake
I have done because this happened while simulating another dimer
also though not sever. Hence I seek some guidance from this
community regarding the problem. I attach the graph herewith.
Kindly help. Let me know if I need to give any other information.

Please see my post from yesterday for a more detailed reply to this exact
same type of question. I am beginning to suspect there's a problem with
g_mindist, but I have no solid evidence for that claim, just a hunch. It
looks like your protein crosses a periodic boundary and that messes up the
calculation. Please center the protein in the box with trjconv -center and
re-analyze to see if there are any differences.

-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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

==**==
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/**
Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore
posting!
Please don't post (un)subscribe requests to the list. Use the www interface
or send it to gmx-users-requ...@gromacs.org.
Can't post? Read
http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists

--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] (no subject)


-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] New maintenance release: 4.5.5

2011-09-21 Thread Rossen Apostolov


Dear Gromacs community,

A new maintenance release of Gromacs is available for download at 
ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.5.5.tar.gz.


Some notable updates in this release:

 * Improved pdb2gmx -chainsep option and reintroduced the -merge option.
 * Fixed mdrun file appending truncating files to 0 bytes when
   continuation runs stopped before writing new output.
 * Fixed COM pulling with multiple constraints checking the convergence
   of one constraint instead of all.
 * Fixed some dihedrals in sugars in Gromos53a5/6 working on the wrong
   atoms.
 * AmberGS force field is now based on Amber94 instead of Amber96.
 * Moved hydrogens in Charmm27 protein termini to separate charge
   groups and added ACE and CT3 residue types.
 * Many small fixes which avoid termination with fatal errors or
   crashes in mdrun and tools.
 * Many small updates to the manual pages of programs.


Big thanks to all developers and users!

Happy simulating!
Rossen
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] question about martini coarse-grained

Dear Gromacs Users,



I want to simulate 150 surfactant molecules in the water by MARTINI 
Coarse-Grained force field, and I have several questions please:
1- I defined 2 groups in index.ndx file named surfactants
  and w_ion_ wf that second group is consist of water,
  antifreeze water and ions. Is my definition good for index
  file?
2- For add the water and antifreeze water to my system, I use
  the gro file of water (consist of 400 W) in MARTINI site for
  both of them, but in the second one (antifreeze water), I
  changed W to WF in this file. Is it right?
3- When I minimize my system, in the first steps of
  minimization, potential is a large positive number and when
  converge to Fmax, it is a negative large number from 10e+05,
  but when I work with gromos96 force field, the first steps of
  minimization are negative. Is it a problem about my
  minimization with MARTINI Coarse-Grained? and what do I do
  please?   
4- For equilibrium step in simulation, I want that restraint
  my surfactant molecules, so, I made a posre.itp for
  surfactant molecules by genrestr program, but when I run a
  pr.mdp for 20ns to density adjustment, my surfactant
  molecules are assembled and is made micelle, while I want to
  remain in random place in primary state!!! what do I do?
Please help me.

Best Regards
Sara-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] question about martini coarse-grained

Dear Gromacs Users,



I want to simulate 150 surfactant molecules in the water by MARTINI 
Coarse-Grained force field, and I have several questions please:
1- I defined 2 groups in index.ndx file named surfactants
  and w_ion_ wf that second group is consist of water,
  antifreeze water and ions. Is my definition good for index
  file?
2- For add the water and antifreeze water to my system, I use
  the gro file of water (consist of 400 W) in MARTINI site for
  both of them, but in the second one (antifreeze water), I
  changed W to WF in this file. Is it right?
3- When I minimize my system, in the first steps of
  minimization, potential is a large positive number and when
  converge to Fmax, it is a negative large number from 10e+05,
  but when I work with gromos96 force field, the first steps of
  minimization are negative. Is it a problem about my
  minimization with MARTINI Coarse-Grained? and what do I do
  please?   
4- For equilibrium step in simulation, I want that restraint
  my surfactant molecules, so, I made a posre.itp for
  surfactant molecules by genrestr program, but when I run a
  pr.mdp for 20ns to density adjustment, my surfactant
  molecules are assembled and is made micelle, while I want to
  remain in random place in primary state!!! what do I do?
Please help me.

Best Regards
Sara-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] GROMACS @ Facebook

2011-09-21 Thread David van der Spoel


Hi,

for your entertainment and as a reach-out to younger scientists GROMACS 
is now on Facebook. Please look us up at:


http://www.facebook.com/pages/GROMACS/257453660934850

We're looking forward to your comments.

Cheers,
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell  Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] Error mesage

2011-09-21 Thread Tanos Franca


Dear gmx users,
Does someone know how to deal with the error mesage bellow ?
With my best regards,
Tanos C. C. Franca.

Program mdrun, VERSION 4.5.4
Source code file: domdec_con.c, line: 693

Fatal error:
DD cell 2 1 0 could only obtain 273 of the 275 atoms that are connected 
via constraints from the neighboring cells. This probably means your 
constraint lengths are too long compared to the domain decomposition 
cell size. Decrease the number of domain decomposition grid cells or 
lincs-order.

--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Error mesage




Tanos Franca wrote:

Dear gmx users,
Does someone know how to deal with the error mesage bellow ?


The DD geometry depends upon the configuration of the system, constraints 
applied, cutoffs, and any other special restraints (like distance restraints) 
that may be present.  The error message suggests that you decrease the number of 
DD cells, which I would suggest you try.  This makes each DD cell larger and 
thus capable of handling longer interactions.  There are minimum size limits 
defined in the log file; if the system changes much then these can become invalid.


-Justin


With my best regards,
Tanos C. C. Franca.

Program mdrun, VERSION 4.5.4
Source code file: domdec_con.c, line: 693

Fatal error:
DD cell 2 1 0 could only obtain 273 of the 275 atoms that are connected 
via constraints from the neighboring cells. This probably means your 
constraint lengths are too long compared to the domain decomposition 
cell size. Decrease the number of domain decomposition grid cells or 
lincs-order.


--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] Temperature for different groups

2011-09-21 Thread Marcelino Arciniega Castro

Hi everybody,

I have a small question. I read somewhere that for a better performance on 
coupling the Temperature of a system is better do it by dividing the system in 
groups, let say protein and solvent, and coupling them to the same target 
temperature. Is it remaining true for other integrator than md, e.g. sd. 
Thanks in advance,
Marcelino
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Temperature for different groups


On 22/09/2011 1:22 AM, Marcelino Arciniega Castro wrote:

Hi everybody,

I have a small question. I read somewhere that for a better performance on 
coupling the Temperature of a system is better do it by dividing the system in 
groups, let say protein and solvent, and coupling them to the same target 
temperature. Is it remaining true for other integrator than md, e.g. sd.


I don't know about SD, but conventional advice about T coupling may well 
be out of date. Do check out the GROMACS manual section, and 
particularly its reference 33.


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

[gmx-users] Re: GROMACS @ Facebook

2011-09-21 Thread Dr. Vitaly V. Chaban

Cool... :-)

 Hi,

 for your entertainment and as a reach-out to younger scientists GROMACS
 is now on Facebook. Please look us up at:

 http://www.facebook.com/pages/GROMACS/257453660934850

 We're looking forward to your comments.

 Cheers,
 --
 David van der Spoel, Ph.D., Professor of Biology
 Dept. of Cell  Molec. Biol., Uppsala University.
 Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
 sp...@xray.bmc.uu.se    http://folding.bmc.uu.se
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] question about position restraint in martini coarse-grained

Dear Gromacs Users,



I want to simulate 150 surfactant molecules in the water by MARTINI 
Coarse-Grained force field, and I have several questions please:
1- I defined 2 groups in index.ndx file named surfactants
  and w_ion_ wf that second group is consist of water,
  antifreeze water and ions. Is my definition good for index
  file?
2- For add the water and antifreeze water to my system, I use
  the gro file of water (consist of 400 W) in MARTINI site for
  both of them, but in the second one (antifreeze water), I
  changed W to WF in this file. Is it right?
3- When I minimize my system, in the first steps of
  minimization, potential is a large positive number and when
  converge to Fmax, it is a negative large number from 10e+05,
  but when I work with gromos96 force field, the first steps of
  minimization are negative. Is it a problem about my
  minimization with MARTINI Coarse-Grained? and what do I do
  please?   
4- For equilibrium step in simulation, I want that restraint
  my surfactant molecules, so, I made a posre.itp for
  surfactant molecules by genrestr program, but when I run a
  pr.mdp for 20ns to density adjustment, my surfactant
  molecules are assembled and is made micelle, while I want to
  remain in random place in primary state!!! what do I do?
Please help me.

Best Regards
Sara-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] meaning of minus potential and buried surface area

2011-09-21 Thread ahmet yıldırım

Dear users,

1.) During the simulation the mean potential energy is minus (-) value. What
does this mean? Why minus?
2.) let's say, Interface/Buried Surace Area (ISA) between protein and ligand
was calculated and hydrophobic ISA obtained greater than hydrophilic ISA.
What does this mean?

No one is my special advisor but If you help me, I will be happy.

Thanks in advance

-- 
Ahmet YILDIRIM
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] sd integrator

2011-09-21 Thread Sai Pooja

Hi,

The sd integrator is described in the manual as follows:
sd
An accurate leap-frog stochastic dynamics integrator. Four Gaussian
random number are required per integration step per degree of freedom.
With constraints, coordinates needs to be constrained twice per
integration step. Depending on the computational cost of the force
calculation, this can take a significant part of the simulation time.
The temperature for one or more groups of atoms (tc_grps) is set with
ref_t [K], the inverse friction constant for each group is set with
tau_t [ps]. The parameter tcoupl is ignored. The random generator is
initialized with ld_seed. When used as a thermostat, an appropriate
value for tau_t is 2 ps, since this results in a friction that is
lower than the internal friction of water, while it is high enough to
remove excess heat (unless cut-off or reaction-field electrostatics is
used). NOTE: temperature deviations decay twice as fast as with a
Berendsen thermostat with the same tau_t.

It is not clear what is the purpose of this integrator and how is it
different from ld. Can someone refer me to a paper?
Can such an integrator help in making trajectories less deterministic?

Pooja

-- 
Quaerendo Invenietis-Seek and you shall discover.
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] meaning of minus potential and buried surface area




ahmet yıldırım wrote:

Dear users,

1.) During the simulation the mean potential energy is minus (-) value. 
What does this mean? Why minus?


Net attraction.

2.) let's say, Interface/Buried Surace Area (ISA) between protein and 
ligand was calculated and hydrophobic ISA obtained greater than 
hydrophilic ISA. What does this mean?




That, as you might expect, hydrophobic groups are shielded from the solvent to a 
greater extent than polar groups.


-Justin


No one is my special advisor but If you help me, I will be happy.

Thanks in advance

--
Ahmet YILDIRIM



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] particle decomp crashes while domain decomp does not

2011-09-21 Thread Florian Altvater

Hi,
I don't know if my question somehow got lost, or if I forgot to provide
some necessary information. Anyway it would be of great help to me, if
someone could tell me her/his opinion on the problem. I need to use
particle decomposition as I want to introduce distance restraints from
2-6nm, which domain decomposition can't handle apparently.

Thanks again for your help
Florian

Am 19.09.2011 14:30, schrieb Florian Altvater:
 Hi there,
 I haven't found a post describing this problem, so here I am.

 I'm running GROMACS 4.3.5 with the OPLS-AA force-field and the TIP3P
 water model on a 170kDa protein dimer with sodium ions to neutralize the
 charges. I added two new residues to the force-field (which seem to
 behave normally). Now the problem:

 When I run with domain decomposition everything works fine during 9ns.
 The structure seems to equilibrate more or less and the overall domain
 conformation doesn't seem to alter much.

 When I switch on particle decomposition, however, the simulation crashes
 after 2-3ns due to a lincs warning. It seems to happen always at the
 same residue, Arg318 which gets pulled/pushed out of the helix it is in.
 The closest modified residue is 326 which doesn't seem to be disturb the
 system too much.

 Anyway it seems strange to me that the method of decomposition seems to
 change the outcome of the simulation a lot (and does not only reflect in
 the computing time). Now I don't understand too much of the algorithms
 used. And as I couldn't find anything bout adjusting parameters if using
 the one or the other I'm a bit in the dark about what to do now.

 Did you have similar experiences? How do you suggest that I tackle the
 problem? Do you need more information? In case it is of any relevance
 here the parameters of the mdp file:

 dt   = 0.002
 nsteps   = 150
 comm-grps= system
 nstxout  = 2
 nstvout  = 2
 nstfout  = 2
 nstlog   = 2
 nstcalcenergy= 1
 nstxtcout= 500
 xtc-grps = protein
 energygrps   = protein
 ns_type  = grid
 rlist= 1.0
 coulombtype  = PME
 vdw-type  = Cut-off
 rcoulomb = 1.0
 rvdw = 1.0
 DispCorr = EnerPres
 tcoupl   = V-rescale
 tc-grps  = Protein Non-Protein
 tau_t= 0.10.1
 ref_t= 325 325
 pcoupl   = Parrinello-Rahman
 pcoupltype   = isotropic
 tau_p= 2.0
 compressibility  = 4.5e-5
 ref_p= 1.0
 andersen_seed= -1
 gen_vel  = no
 gen-temp = 325
 gen-seed = -1
 constraints  = all-bonds
 constraint_algorithm = lincs
 continuation = yes
 lincs_order  = 4
 lincs_iter   = 1
 disre= simple
 disre_weighting  = conservative
 disre_fc = 800
 disre_tau= 0


 Thank you very much.
 Regards,
 Florian



-- 
Florian Altvater
Albert-Ludwigs-Universität Freiburg
Institut für Physikalische Chemie - Lehrstuhl I
Albertstr. 21
79104 Freiburg, Germany

Phone: +49 (761) 203-6210
Fax: +49 (761) 203-6222
E-Mail: florian.altva...@physchem.uni-freiburg.de

-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] sd integrator


On 22/09/2011 6:21 AM, Sai Pooja wrote:

Hi,

The sd integrator is described in the manual as follows:
sd
An accurate leap-frog stochastic dynamics integrator. Four Gaussian
random number are required per integration step per degree of freedom.
With constraints, coordinates needs to be constrained twice per
integration step. Depending on the computational cost of the force
calculation, this can take a significant part of the simulation time.
The temperature for one or more groups of atoms (tc_grps) is set with
ref_t [K], the inverse friction constant for each group is set with
tau_t [ps]. The parameter tcoupl is ignored. The random generator is
initialized with ld_seed. When used as a thermostat, an appropriate
value for tau_t is 2 ps, since this results in a friction that is
lower than the internal friction of water, while it is high enough to
remove excess heat (unless cut-off or reaction-field electrostatics is
used). NOTE: temperature deviations decay twice as fast as with a
Berendsen thermostat with the same tau_t.

It is not clear what is the purpose of this integrator and how is it
different from ld. Can someone refer me to a paper?


See manual section 3.8 and ref therein.


Can such an integrator help in making trajectories less deterministic?


It's still going to be deterministic, because the RNG is.

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

Re: [gmx-users] sd integrator

2011-09-21 Thread Sai Pooja

But is the effect of varying ld_seed.. can that make different
trajectories stochastic?



On Wed, Sep 21, 2011 at 7:40 PM, Mark Abraham mark.abra...@anu.edu.au wrote:
 On 22/09/2011 6:21 AM, Sai Pooja wrote:

 Hi,

 The sd integrator is described in the manual as follows:
 sd
 An accurate leap-frog stochastic dynamics integrator. Four Gaussian
 random number are required per integration step per degree of freedom.
 With constraints, coordinates needs to be constrained twice per
 integration step. Depending on the computational cost of the force
 calculation, this can take a significant part of the simulation time.
 The temperature for one or more groups of atoms (tc_grps) is set with
 ref_t [K], the inverse friction constant for each group is set with
 tau_t [ps]. The parameter tcoupl is ignored. The random generator is
 initialized with ld_seed. When used as a thermostat, an appropriate
 value for tau_t is 2 ps, since this results in a friction that is
 lower than the internal friction of water, while it is high enough to
 remove excess heat (unless cut-off or reaction-field electrostatics is
 used). NOTE: temperature deviations decay twice as fast as with a
 Berendsen thermostat with the same tau_t.

 It is not clear what is the purpose of this integrator and how is it
 different from ld. Can someone refer me to a paper?

 See manual section 3.8 and ref therein.

 Can such an integrator help in making trajectories less deterministic?

 It's still going to be deterministic, because the RNG is.

 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/Support/Mailing_Lists/Search before posting!
 Please don't post (un)subscribe requests to the list. Use the www interface
 or send it to gmx-users-requ...@gromacs.org.
 Can't post? Read http://www.gromacs.org/Support/Mailing_Lists




-- 
Quaerendo Invenietis-Seek and you shall discover.
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] sd integrator


On 22/09/2011 9:57 AM, Sai Pooja wrote:

But is the effect of varying ld_seed.. can that make different
trajectories stochastic?


Any single MD or SD trajectory is literally stochastic. Either can start 
from the same point with respectively different ld_seed or gen_seed and 
diverge.


Mark



On Wed, Sep 21, 2011 at 7:40 PM, Mark Abrahammark.abra...@anu.edu.au  wrote:

On 22/09/2011 6:21 AM, Sai Pooja wrote:

Hi,

The sd integrator is described in the manual as follows:
sd
An accurate leap-frog stochastic dynamics integrator. Four Gaussian
random number are required per integration step per degree of freedom.
With constraints, coordinates needs to be constrained twice per
integration step. Depending on the computational cost of the force
calculation, this can take a significant part of the simulation time.
The temperature for one or more groups of atoms (tc_grps) is set with
ref_t [K], the inverse friction constant for each group is set with
tau_t [ps]. The parameter tcoupl is ignored. The random generator is
initialized with ld_seed. When used as a thermostat, an appropriate
value for tau_t is 2 ps, since this results in a friction that is
lower than the internal friction of water, while it is high enough to
remove excess heat (unless cut-off or reaction-field electrostatics is
used). NOTE: temperature deviations decay twice as fast as with a
Berendsen thermostat with the same tau_t.

It is not clear what is the purpose of this integrator and how is it
different from ld. Can someone refer me to a paper?

See manual section 3.8 and ref therein.


Can such an integrator help in making trajectories less deterministic?

It's still going to be deterministic, because the RNG is.

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






--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] particle decomp crashes while domain decomp does not


On 22/09/2011 8:45 AM, Florian Altvater wrote:

Hi,
I don't know if my question somehow got lost, or if I forgot to provide
some necessary information. Anyway it would be of great help to me, if
someone could tell me her/his opinion on the problem. I need to use
particle decomposition as I want to introduce distance restraints from
2-6nm, which domain decomposition can't handle apparently.

Thanks again for your help
Florian

Am 19.09.2011 14:30, schrieb Florian Altvater:

Hi there,
I haven't found a post describing this problem, so here I am.

I'm running GROMACS 4.3.5 with the OPLS-AA force-field and the TIP3P
water model on a 170kDa protein dimer with sodium ions to neutralize the
charges. I added two new residues to the force-field (which seem to
behave normally). Now the problem:

When I run with domain decomposition everything works fine during 9ns.
The structure seems to equilibrate more or less and the overall domain
conformation doesn't seem to alter much.

When I switch on particle decomposition, however, the simulation crashes
after 2-3ns due to a lincs warning. It seems to happen always at the
same residue, Arg318 which gets pulled/pushed out of the helix it is in.
The closest modified residue is 326 which doesn't seem to be disturb the
system too much.

Anyway it seems strange to me that the method of decomposition seems to
change the outcome of the simulation a lot (and does not only reflect in
the computing time). Now I don't understand too much of the algorithms
used. And as I couldn't find anything bout adjusting parameters if using
the one or the other I'm a bit in the dark about what to do now.

Did you have similar experiences? How do you suggest that I tackle the
problem? Do you need more information? In case it is of any relevance
here the parameters of the mdp file:

 dt   = 0.002
 nsteps   = 150
 comm-grps= system
 nstxout  = 2
 nstvout  = 2
 nstfout  = 2
 nstlog   = 2
 nstcalcenergy= 1
 nstxtcout= 500
 xtc-grps = protein
 energygrps   = protein
 ns_type  = grid
 rlist= 1.0
 coulombtype  = PME
 vdw-type  = Cut-off
 rcoulomb = 1.0
 rvdw = 1.0
 DispCorr = EnerPres
 tcoupl   = V-rescale
 tc-grps  = Protein Non-Protein
 tau_t= 0.10.1
 ref_t= 325 325
 pcoupl   = Parrinello-Rahman
 pcoupltype   = isotropic
 tau_p= 2.0
 compressibility  = 4.5e-5
 ref_p= 1.0
 andersen_seed= -1
 gen_vel  = no
 gen-temp = 325
 gen-seed = -1
 constraints  = all-bonds
 constraint_algorithm = lincs
 continuation = yes
 lincs_order  = 4
 lincs_iter   = 1
 disre= simple
 disre_weighting  = conservative
 disre_fc = 800
 disre_tau= 0


The different decomposition algorithm can be enough for the chaotic 
simulation to diverge enough that a marginally stable situation can 
either explode or move to a stable point. However Parrinello-Rahman is 
also unsuitable for equilibration, and that could perhaps amplify the 
former effect. Equilibrate with Berendsen, and if you still encounter PD 
vs DD issues, please try again with the latest 4.5.5 release.


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

Re: [gmx-users] problem in compiling GMX with MPI


On 21/09/2011 7:59 PM, Jinan Niu wrote:


Hi, everyone:
when I compiled GMX4.5.5, I encountered a problem and failed many 
times, SOS!

Below is my config.log:


More useful would be the information that you've been following the 
online installation guide, and what your configure line was. As it is, 
it looks like you have some problem with the compiler. Can you compile 
other code?


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

Re: [gmx-users] error while install GMX4.5.5


On 21/09/2011 7:27 PM, zhongjin wrote:

Dear GMX users:
While I am installing gmx4.5.5, an error occured after make command :
cc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused 
-msse2 -funroll-all-loops -std=gnu99 -pthread -I./include -o 
.libs/grompp grompp.o  -L/home/hzj1000/software/fftw/lib 
./.libs/libgmxpreprocess.so 
/home/hzj1000/gromacs-4.5.5/src/mdlib/.libs/libmd.so 
../mdlib/.libs/libmd.so 
/home/hzj1000/gromacs-4.5.5/src/gmxlib/.libs/libgmx.so 
../gmxlib/.libs/libgmx.so -ldl -lnsl -lm  -Wl,--rpath 
-Wl,/home/hzj1000/software/GMX/gromacs4.5.5/lib
/home/hzj1000/gromacs-4.5.5/src/gmxlib/.libs/libgmx.so: undefined 
reference to `pthread_setaffinity_np'

collect2: ld returned 1 exit status
make[3]: *** [grompp] Error 1
make[3]: Leaving directory `/home/hzj1000/gromacs-4.5.5/src/kernel'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/home/hzj1000/gromacs-4.5.5/src'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/home/hzj1000/gromacs-4.5.5/src'



This shouldn't happen. What compiler and hardware? configure or CMake? 
What command lines?


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

Re: [gmx-users] Replex in REMD