Re: [gmx-users] Free Energy Calculations in Gromacs

[HANNIBAL LECTER]

Thank you Professor Shirts.

So now my protein itp file looks like this:
[ atoms ]
;   nrtype  resnr residue  atom  cgnr  chargemasstypeB
 chargeB  MassB
 1 CT1ACECH3  1   -0.190264   12.01  CT_per
-0.12033412.01

[ bonds ]
;ai  aj func th0 kb th0B kbB
1 2  1   0.10900  284512.0   0.10900113804.8


[ pairs ]
1 8 1


[ angles ]
;ai   ajak  funct  th0 kb th0B  kbB
2 1 3  1   109.500  292.880   109.500117.152
.

[ dihedrals ]
ij kl func th0   cth mult  th0B cthB
   multB
2 1 5 6   9180.0 2.86144  1180.01.14458  1

Now, I have created 6 different lambda values and placed a
well-equilibrated structure and the same topology file (with values
corresp. to lambda=0 and lambda =1) within six directories. The .mdp files
contain the information (init-lambda-state=0,1,..) which lambda state is
it.

Is my approach correct ?

Secondly, when I grompp followed by gmxdump -s *.tpr I find, that there is
no difference in hamiltonian between the two. So, does the scaling take
place during runtime?

Third, since in state B only the hamiltonian is rescaled (the perturbed
entries are defined in ffnonbonded.itp file) do I need to explicitly add
another section [ pairs_nb ]?

Again, I thank you for replying.



On Sat, Apr 20, 2013 at 5:52 PM, Michael Shirts  wrote:

> You have to change atom types.  For example:
>
> [ atomtypes ]
> ;name  bond_typemasscharge   ptype  sigma  epsilon
> h1h1 0.  0.  A  2.47135e-01
>  6.56888e-02
> h1_pert h1 0.  0.  A  2.47135e-01  3.56888e-02
> ; perturbed
>
> The mass and charge can be zero, because they will be defined in the [
> atoms ] part
>
> [ atoms ]
> ;   nrtype  resnr residue  atom  cgnr  chargemasstypeB
>  chargeB  MassB
> 1 h1  1 BLAHH1a 1 -0.0891.008h1_pert
>  -0.030  1.008;  perturbed
>
>
>
> On Sat, Apr 20, 2013 at 4:04 PM, HANNIBAL LECTER <
> hanniballecte...@gmail.com
> > wrote:
>
> > Hi,
> >
> > I am trying to perform expanded ensemble simulations between 2 states A
> > (lambda=0) and B (lambda =1) with 6 intermediate lambda values.
> >
> > In state B the Hamiltonian is rescaled, such that the epsilons of the vdW
> > interactions, the charges, the bond, angle and dihedral constants are a
> > multiple of the similar terms of State A.
> >
> > It's not quite clear to me (going through the archives of the gmx-users
> > mailing list how to perform these calculations. One way to do this, is to
> > use a single topology file in which the charges and the other terms are
> > specified for both states A and B. However, it is not clear as to how
> > should I scale the epsilons in the topology file. (My atoms are not
> mutated
> > in state B. They are the same atoms with scaled epsilons.)
> >
> > Secondly, since I have the topology files for states A and B, is there a
> > way I could perform the simulations (any particular way in grompp) where
> > both the topology files can be preprocessed designating the end states
> and
> > using the mdp options, the simulations corresponding to the intermediate
> > lambda values performed??
> > --
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Re: [gmx-users] any other criteria for h-bond?

[Erik Marklund]

Hi,

Could you please clarify if the hbond existed in frames for which g_sdangle 
reported a ADH-angle above 30 deg?

Also, bear in mind that the -merge flag is on by default, so another hydrogen 
may bridge the donor-acceptor gap.

Erik

On 24 Apr 2013, at 21:09, kim2811  wrote:

> Hi, is there any other criteria in determining a hydrogen bond? i know that
> in order for a bond to exist, donor-acceptor distance should be less than
> or equal 3.5A and A-D-H angle less than or equal 30deg. I used g_sgangle to
> measure the angle A-D-H of two hydrogen bonds identified when I determined
> the hydrogen bonds using g_hbond. What I did is, I separated A-D and H-D as
> two groups (i made the atom indices in the order A-D and H-D in the index
> file) and measured the angle between these two vectors. However, the A-D-H
> angle as a function of time fall above the cut-off of 30deg and I wonder
> why. is there any other explanation for this?
> 
> thank you.
> 
> -- 
> Kristine
> 
> 
> 
> 
> --
> View this message in context: 
> http://gromacs.5086.x6.nabble.com/any-other-criteria-for-h-bond-tp5007623.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
> -- 
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[gmx-users] any other criteria for h-bond?

[kim2811]

Hi, is there any other criteria in determining a hydrogen bond? i know that
in order for a bond to exist, donor-acceptor distance should be less than
or equal 3.5A and A-D-H angle less than or equal 30deg. I used g_sgangle to
measure the angle A-D-H of two hydrogen bonds identified when I determined
the hydrogen bonds using g_hbond. What I did is, I separated A-D and H-D as
two groups (i made the atom indices in the order A-D and H-D in the index
file) and measured the angle between these two vectors. However, the A-D-H
angle as a function of time fall above the cut-off of 30deg and I wonder
why. is there any other explanation for this?

thank you.

-- 
Kristine




--
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[gmx-users] How to use multiple nodes, each with 2 CPUs and 3 GPUs

[Christopher Neale]

Dear Users:

I am having trouble getting any speedup by using more than one node, 
where each node has 2 8-core cpus and 3 GPUs. I am using gromacs 4.6.1.

I saw this post, indicating that the .log file output about number of gpus used 
might not be accurate:
http://lists.gromacs.org/pipermail/gmx-users/2013-March/079802.html

Still, I'm getting 21.2 ns/day on 1 node, 21.2 ns/day on 2 nodes, and 20.5 
ns/day on 3 nodes. 
Somehow I think I have not configures the mpirun -np and mdrun -ntomp correctly 
(although I have tried numerous combinations).

On 1 node, I can just run mdrun without mpirun like this:
http://lists.gromacs.org/pipermail/gmx-users/2013-March/079802.html

For that run, the top of the .log file is:
Log file opened on Wed Apr 24 11:36:53 2013
Host: kfs179  pid: 59561  nodeid: 0  nnodes:  1
Gromacs version:VERSION 4.6.1
Precision:  single
Memory model:   64 bit
MPI library:thread_mpi
OpenMP support: enabled
GPU support:enabled
invsqrt routine:gmx_software_invsqrt(x)
CPU acceleration:   AVX_256
FFT library:fftw-3.3.3-sse2
Large file support: enabled
RDTSCP usage:   enabled
Built on:   Tue Apr 23 12:59:48 EDT 2013
Built by:   cne...@kfslogin2.nics.utk.edu [CMAKE]
Build OS/arch:  Linux 2.6.32-220.4.1.el6.x86_64 x86_64
Build CPU vendor:   GenuineIntel
Build CPU brand:Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz
Build CPU family:   6   Model: 45   Stepping: 7
Build CPU features: aes apic avx clfsh cmov cx8 cx16 htt lahf_lm mmx msr 
nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1 
sse4.2 ssse3 tdt x2apic
C compiler: /opt/intel/composer_xe_2011_sp1.11.339/bin/intel64/icc 
Intel icc (ICC) 12.1.5 20120612
C compiler flags:   -mavx   -std=gnu99 -Wall   -ip -funroll-all-loops  -O3 
-DNDEBUG
C++ compiler:   /opt/intel/composer_xe_2011_sp1.11.339/bin/intel64/icpc 
Intel icpc (ICC) 12.1.5 20120612
C++ compiler flags: -mavx   -Wall   -ip -funroll-all-loops  -O3 -DNDEBUG
CUDA compiler:  nvcc: NVIDIA (R) Cuda compiler driver;Copyright (c) 
2005-2012 NVIDIA Corporation;Built on Thu_Apr__5_00:24:31_PDT_2012;Cuda 
compilation tools, release 4.2, V0.2.1221
CUDA driver:5.0
CUDA runtime:   4.20
...

...
Initializing Domain Decomposition on 3 nodes
Dynamic load balancing: yes
Will sort the charge groups at every domain (re)decomposition
Initial maximum inter charge-group distances:
two-body bonded interactions: 0.431 nm, LJ-14, atoms 101 108
  multi-body bonded interactions: 0.431 nm, Proper Dih., atoms 101 108
Minimum cell size due to bonded interactions: 0.475 nm
Maximum distance for 7 constraints, at 120 deg. angles, all-trans: 1.175 nm
Estimated maximum distance required for P-LINCS: 1.175 nm
This distance will limit the DD cell size, you can override this with -rcon
Using 0 separate PME nodes, per user request
Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
Optimizing the DD grid for 3 cells with a minimum initial size of 1.469 nm
The maximum allowed number of cells is: X 5 Y 5 Z 6
Domain decomposition grid 3 x 1 x 1, separate PME nodes 0
PME domain decomposition: 3 x 1 x 1
Domain decomposition nodeid 0, coordinates 0 0 0

Using 3 MPI threads
Using 5 OpenMP threads per tMPI thread

Detecting CPU-specific acceleration.
Present hardware specification:
Vendor: GenuineIntel
Brand:  Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz
Family:  6  Model: 45  Stepping:  7
Features: aes apic avx clfsh cmov cx8 cx16 htt lahf_lm mmx msr nonstop_tsc pcid 
pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
Acceleration most likely to fit this hardware: AVX_256
Acceleration selected at GROMACS compile time: AVX_256


3 GPUs detected:
  #0: NVIDIA Tesla M2090, compute cap.: 2.0, ECC: yes, stat: compatible
  #1: NVIDIA Tesla M2090, compute cap.: 2.0, ECC: yes, stat: compatible
  #2: NVIDIA Tesla M2090, compute cap.: 2.0, ECC: yes, stat: compatible

3 GPUs auto-selected for this run: #0, #1, #2

Will do PME sum in reciprocal space.
...

...

 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   Th. Count  Wall t (s) G-Cycles   %
-
 Domain decomp. 35   4380  23.714  922.574 6.7
 DD comm. load  35   4379   0.0542.114 0.0
 DD comm. bounds35   4381   0.0562.193 0.0
 Neighbor search35   4380  11.325  440.581 3.2
 Launch GPU ops.35  87582   3.970  154.455 1.1
 Comm. coord.   35  39411   2.522   98.132 0.7
 Force  35  43791  55.351 2153.40915.5
 Wait + Comm. F 35  43791   2.800  108.930 0.8
 PME mesh   35  43791  97.377 3788.42727.3
 Wait GPU nonlocal  35  43791  

Re: [gmx-users] Fwd: Selecting the temperature distribution

[massimo sandal]

Don't be sorry. It's okay. It's just cultural differences.


2013/4/24 bharat gupta 

> I think it should be me who should be sorry. I should have asked the
> question again in the forum without referring to some particular
> individual.
>
>
> On Wed, Apr 24, 2013 at 9:30 PM, massimo sandal  >wrote:
>
> > 2013/4/24 Justin Lemkul 
> >
> > >
> > >
> > > I haven't said anything because I agree with what Massimo has already
> > told
> > > you.  If that is comforting in some way to know, then so be it, but I
> > think
> > > it is rather rude to suggest that you would rather someone else answer
> > your
> > > question, even after being given thorough and correct insight.  This
> is a
> > > community forum with many experts who have valuable insight to share.
> > >
> >
> > Well, he couldn't know that my insight was right (honestly, I was
> expecting
> > to be corrected!). I think he did right by trying to be double-sure, I
> > don't feel offended by it :)
> > --
> > 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
> >
>
>
>
> --
> Bharat
> Ph.D. Candidate
> Biomolecular Engineering Laboratory
> Pusan National University
> South Korea
> Mobile no. - 010-5818-3680
> --
> gmx-users mailing listgmx-users@gromacs.org
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[gmx-users] Fwd: amber03 force field

[Elisa Frezza]

Dear All,

I am starting to use amber03 force field, but I have found something very
strange for proper angle dihedral.

On the basis of definition of proper dihedral function in AMBER and GROMACS
manual I aspect that the following conversion from amber to gromacs:

k_n(GROMACS)=4.18/2 V_n (AMBER)

where n= multiplicity.

If I compare ffbonded.itp file in ffamber03 folder and the parameter
reported in amber I find something very strange and I do not understand
what it is right:

   constant   angle
   multiplicity
AMBER:   X   CCNX8.00 180 2
GROMACS   X   CCNX  16.736180 2
   # kn= 4.18/2 V_n

   constant   angle
   multiplicity
AMBER:   X   CNAX5.648 180 2
GROMACS   X   CNAX5.648 180 2
 # kn= 4.18/4 V_n

the ratios between kn and Vn are different.
Have someone some suggestions or explanation?

Thanks in advance

Elisa

-- 
Elisa Frezza
Ph.D. Student in Materials Science and Engineering
Dipartimento di Scienze Chimiche
Università di Padova
via Marzolo, 1
35131 Padova - Italy
Phone: +39 049 827 5149
Skype: elisa.frezza
Emai: elisa.fre...@gmail.com
 elisa.fre...@studenti.unipd.it





-- 
Elisa Frezza
Ph.D. Student in Materials Science and Engineering
Dipartimento di Scienze Chimiche
Università di Padova
via Marzolo, 1
35131 Padova - Italy
Phone: +39 049 827 5149
Skype: elisa.frezza
Emai: elisa.fre...@gmail.com
 elisa.fre...@studenti.unipd.it
--
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[gmx-users] Fwd: amber03 force field

[Elisa Frezza]

Dear All,

I am starting to use amber03 force field, but I have found something very
strange for proper angle dihedral.

On the basis of definition of proper dihedral function in AMBER and GROMACS
manual I aspect that the following conversion from amber to gromacs:

k_n(GROMACS)=4.18/k V_n (AMBER)

where n= multiplicity.

If I compare ffbonded.itp file in ffamber03 folder and the parameter
reported in amber I find something very strange and I do not understand
what it is right:

   constant   angle
 multiplicity
AMBER:   X   CCNX8.00 180 2
GROMACS

-- 
Elisa Frezza
Ph.D. Student in Materials Science and Engineering
Dipartimento di Scienze Chimiche
Università di Padova
via Marzolo, 1
35131 Padova - Italy
Phone: +39 049 827 5149
Skype: elisa.frezza
Emai: elisa.fre...@gmail.com
 elisa.fre...@studenti.unipd.it





-- 
Elisa Frezza
Ph.D. Student in Materials Science and Engineering
Dipartimento di Scienze Chimiche
Università di Padova
via Marzolo, 1
35131 Padova - Italy
Phone: +39 049 827 5149
Skype: elisa.frezza
Emai: elisa.fre...@gmail.com
 elisa.fre...@studenti.unipd.it
--
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[gmx-users] amber03 force field

[Elisa Frezza]

Dear All,

I am starting to use amber03 force field, but I have found something very
strange for proper angle dihedral.

On the basis of definition of proper dihedral function in AMBER and GROMACS
manual I aspect that the following conversion from amber to gromacs:

k_n(GROMACS)=4.18/k V_n (AMBER)

where n= multiplicity.

If I compare ffbonded.itp file in ffamber03 folder and the parameter
reported in amber I find something very strange and I do not understand
what it is right:


AMBER:   X   CCNX


-- 
Elisa Frezza
Ph.D. Student in Materials Science and Engineering
Dipartimento di Scienze Chimiche
Università di Padova
via Marzolo, 1
35131 Padova - Italy
Phone: +39 049 827 5149
Skype: elisa.frezza
Emai: elisa.fre...@gmail.com
 elisa.fre...@studenti.unipd.it
--
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Re: [gmx-users] Fwd: Selecting the temperature distribution

[bharat gupta]

I think it should be me who should be sorry. I should have asked the
question again in the forum without referring to some particular
individual.


On Wed, Apr 24, 2013 at 9:30 PM, massimo sandal wrote:

> 2013/4/24 Justin Lemkul 
>
> >
> >
> > I haven't said anything because I agree with what Massimo has already
> told
> > you.  If that is comforting in some way to know, then so be it, but I
> think
> > it is rather rude to suggest that you would rather someone else answer
> your
> > question, even after being given thorough and correct insight.  This is a
> > community forum with many experts who have valuable insight to share.
> >
>
> Well, he couldn't know that my insight was right (honestly, I was expecting
> to be corrected!). I think he did right by trying to be double-sure, I
> don't feel offended by it :)
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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> www interface or send it to gmx-users-requ...@gromacs.org.
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>



-- 
Bharat
Ph.D. Candidate
Biomolecular Engineering Laboratory
Pusan National University
South Korea
Mobile no. - 010-5818-3680
-- 
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Re: [gmx-users] Fwd: Selecting the temperature distribution

[massimo sandal]

2013/4/24 Justin Lemkul 

>
>
> I haven't said anything because I agree with what Massimo has already told
> you.  If that is comforting in some way to know, then so be it, but I think
> it is rather rude to suggest that you would rather someone else answer your
> question, even after being given thorough and correct insight.  This is a
> community forum with many experts who have valuable insight to share.
>

Well, he couldn't know that my insight was right (honestly, I was expecting
to be corrected!). I think he did right by trying to be double-sure, I
don't feel offended by it :)
-- 
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Re: [gmx-users] Re: protein-ligand interactions in charmm force field

[Justin Lemkul]

On 4/24/13 3:26 AM, James Starlight wrote:

The only possible way to view  representation of the configuration volume
of the ligand was the representation of  all frames of the ligand along the
trajectory. By the way its not quite understand for me  in one case the
measurement of the diffusion coefficient could be better than MSD which is
the measure of the random displacement of the particle itself. ( my current
taks is the examination of the ligand mobility as the rigid-body within
ligand-binding-cavity).

Also I wounder to know about some possible way to measure dynamics of the
non-covalent bonding along the trajectories.

E.g I've defined in index file all polar and aromatic residues of the
ligand-binding pocket. IS there any way to calculate all possible bonds (I
want to measure the lifetime of that bonds as well as its occurrence in
case of different ligands) between ligand and that side-chains along the
trajectory ?



What you're describing are nonbonded interactions, not bonds.  There are a 
variety of quantities you can measure, like hydrogen bonds, contacts, etc.  You 
can post-process to get various autocorrelations and lifetimes.  Again, Chapter 
8 is your friend here.


-Justin

--


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


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Re: [gmx-users] Re: Membrane Simulation

[Justin Lemkul]

On 4/24/13 4:49 AM, Giuseppe wrote:

Dear Justin,

there were for sure some errors in the command, but even having solved them,
the protein still move during the optimization. What I noticed is that the
coordinates of the residues seems to decrease to zero and than "restart"
from a point out from the box. I mean, taking the first atom of the first
residue, after one EM the coordinates were:

1MET  N1   6.100  15.879   0.231

after the second EM were

1MET  N1   5.469  15.262   0.228

after the third EM were

1MET  N1   4.870  14.676   0.225

and so on till the thirteenth EM in which the coordinates were

1MET  N1   0.321  10.201   0.207

after this EM, protein moves off the membrane and the coordinates of the
first atom of the first residue become:

1MET  N1  12.791   9.867   0.206

there is obviously something wrong with the x axis, but what?
The box vectors in this case were  6.23910   6.17970   6.91950 and the
complete editconf command was "editconf -f protein.gro -o protein_newbox.gro
-box 6.23910   6.17970   6.91950 -center 3.20920 2.72175 6.2 -rotate 145 -45
55".


The only way that this is possible is if your protein is much larger than your 
box.  Note that the y-coordinate of the N atom of Met1 begins at nearly 16 nm, 
which is more than twice the box vector in the y-dimension.  I suspect that your 
protein is ill-suited to being positioned within a box of these dimensions.


Note too that centering on z=6.2 almost assuredly places your protein outside 
the box if the z-dimension is 6.9195 nm.


If there are further problems, separate the rotation and placement steps.  I 
don't recall off-hand which operation is done first, but this can be a source of 
complication.  Rotate your configuration first, then position it in a second step.



I also tried to use a larger box, which vectors were 12 12 12, and in this
case the complete editconf command was "editconf -f protein.gro -o
proetin.newbox.gro -box 12 12 12 -center 6 6 8.75 -rotate 145 -45 55" and to
decrease the scaling factor from 4 to 2, but it was useless. I'm sorry to
bother you so much, but I'm stucked with my project. Thank you so much.



A box size of 12 is still incompatible with the coordinates shown above.

-Justin

--


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


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Re: [gmx-users] RMSD from the average structure

[Justin Lemkul]

On 4/24/13 3:06 AM, bipin singh wrote:

Hi all,

Please let me know whether this is the right way to calculate RMSD from the
average structure from a simulation:

g_rmsf -f traj.xtc -s average.pdb -od rmsdev.xvg


average.pdb: is the pdb file produced using -ox option of g_rmsf.



You can calculate RMSD with respect to whatever structure you like, but the 
interpretation and justification for doing so are up to you.


-Justin

--


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


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Re: [gmx-users] Fwd: Selecting the temperature distribution

[Justin Lemkul]

On 4/23/13 9:43 PM, bharat gupta wrote:

Dear Justin/Mark,

I have asked this question previously in the forum, I got some reply from
other members. It will be more useful if you can provide you expert
comments on the same. I am planning to run REMD for a peptide (406 atoms )+
solvent system (27639). The temperature range I selected is from 300 to
500. I want to select appropriate temp. for 56 replicas (as I have 56
processors available). I used the t-remd calculator for temp. generation.
It provided some 200 temp. values. Here are my questions :
1. Is it possible to select equally spaced temp. values from those values ??
2. I checked that reducing the no. of water mol. decreases the temp.
values. What if I reduce the no. of water mol., will if affect the
simulation ??



I haven't said anything because I agree with what Massimo has already told you. 
 If that is comforting in some way to know, then so be it, but I think it is 
rather rude to suggest that you would rather someone else answer your question, 
even after being given thorough and correct insight.  This is a community forum 
with many experts who have valuable insight to share.


-Justin




On Tue, Apr 23, 2013 at 11:15 PM, massimo sandal wrote:


In general, the smaller is your system, the less temperatures you will need
(and you'll have better performance).

Notice however that implicit solvent, while surely a possibility worth
considering, is not usually considered to be very good -take care that if
you write a paper from implicit solvent results, reviewers might not be
happy. There is a chance that the results coming out of your simulation
might be nonsense. Discuss this choice with your supervisor and/or with
expert colleagues who know about limitations of implicit solvent. You need
to be able to justify your choice scientifically -for example testing it
with a known,similar system and observing that implicit solvent reproduces
the behaviour of that system in explicit solvent well.

About reducing the box size, by all means try it, but always make sure it
is large enough to avoid that the periodic copies of your molecule see each
other. See

http://ringo.ams.sunysb.edu/index.php/MD_Simulation:_Protein_in_Water#Box_Preparationand
be sure to understand it.


2013/4/23 bharat gupta 


Thanks a lot for your prompt responses. By using implicit solvent , I am
getting on 9 temperature values. I think this should work , I will try it
out. Also, i checked that when the no. of water molecules are reduced ,

the

no. of temp. values are also reduced. If I reduce the no. of water
molecules or reduce the size of box , will it help. As of now I am using
octahedron box.


On Tue, Apr 23, 2013 at 10:43 PM, massimo sandal 
wrote:



It depends on what you want to do. Possible it is certainly possible,

but

you can't be guaranteed to observe the conformational changes you

desire

to

observe. Again, it does not depend only on the REMD, but also on the

length

of it. How long will it be? 10 ns? 100? 1000? 10.000? Plus, it also

depends

on your system itself -and this you cannot know without trying.

If you want to improve sampling beyond what standard REMD can do, to
exploit your computational resources at the best, you can look into

other

approaches like solute tempering (
http://www.pnas.org/content/102/39/13749.abstract ), or metadynamics (
http://en.wikipedia.org/wiki/Metadynamics ). However I advise you to

study

*well* this kind of things, talk with experts in these techniques,  and
remember that there is no guarantee any of them will bring the result

you

want. Good luck! :)




2013/4/23 bharat gupta 


So, my final question is whether is possible to do REMD for my

system,

using the computational resource that I have.


On Tue, Apr 23, 2013 at 10:06 PM, massimo sandal <

deviceran...@gmail.com

wrote:



Who knows? It depends on the size of your peptide, on the energy

landscape,

on how long is the run you plan to do. I would bet on "no",

however.



2013/4/23 bharat gupta 


But if I choose a smaller temperature range , would it be

possible

to

observe any folding event ??


On Tue, Apr 23, 2013 at 9:16 PM, massimo sandal <

deviceran...@gmail.com

wrote:



Thanks, now it's clearer.


Now, how can I temp. from these, so that the replicas can

exchange

...


You can't, I would say. The system you have requires so many

replicas

to

exchange properly from the two temperature extremes you set up.

As

you

have

seen, if you pick up temperatures in that range randomly, they

can't

exchange anymore. They are too far away.

I would choose a smaller temperature range. There is little

else

you

can

do, I think.


2013/4/23 bharat gupta 


Sorry for that, I explain it again. Actually, I used the this

link

to

generate a temp. distribution. But I can do REMD for 56

replicas

only,

as I

have 56 processors available. The t-remd calculator provides

220

temperature values :

300.00, 301.01, 302.02, 303.04, 304.06, 305.08, 306.11,

[gmx-users] Funnel Metadynamics using PLUMED/Gromacs

[Davide Mercadante]

Dear gmx/plumed developers,

I know that this is probably a question for the PLUMED mailing list more
than the GMX mailing list but considering that the question involves GROMACS
as well I thought to post it here first.

I have read with great attention the paper by Limongelli et al. published on
the previous issue of PNAS (PNAS (2013) 110; no 16 pp. 6358-6363 -
http://www.pnas.org/content/early/2013/04/03/1303186110.abstract) regarding
the possibility to perform Funnel metadynamics (FM) to study molecular
interactions and more precisely drug binding. I was wondering if plumed, in
its latest or previous versions, supports funnel dynamics and (if yes) I can
do FM patching it with GROMACS.

Thank you and sorry if this is somehow a redundant question.

Regards, 
Davide 

 



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[gmx-users] Re: Membrane Simulation

[Giuseppe]

Dear Justin,

there were for sure some errors in the command, but even having solved them,
the protein still move during the optimization. What I noticed is that the
coordinates of the residues seems to decrease to zero and than "restart"
from a point out from the box. I mean, taking the first atom of the first
residue, after one EM the coordinates were:

1MET  N1   6.100  15.879   0.231

after the second EM were

1MET  N1   5.469  15.262   0.228

after the third EM were

1MET  N1   4.870  14.676   0.225

and so on till the thirteenth EM in which the coordinates were

1MET  N1   0.321  10.201   0.207

after this EM, protein moves off the membrane and the coordinates of the
first atom of the first residue become:

1MET  N1  12.791   9.867   0.206

there is obviously something wrong with the x axis, but what?
The box vectors in this case were  6.23910   6.17970   6.91950 and the
complete editconf command was "editconf -f protein.gro -o protein_newbox.gro
-box 6.23910   6.17970   6.91950 -center 3.20920 2.72175 6.2 -rotate 145 -45
55".
I also tried to use a larger box, which vectors were 12 12 12, and in this
case the complete editconf command was "editconf -f protein.gro -o
proetin.newbox.gro -box 12 12 12 -center 6 6 8.75 -rotate 145 -45 55" and to
decrease the scaling factor from 4 to 2, but it was useless. I'm sorry to
bother you so much, but I'm stucked with my project. Thank you so much.


Yours sincerely,  

GIuseppe 



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Re: [gmx-users] Re: protein-ligand interactions in charmm force field

[James Starlight]

The only possible way to view  representation of the configuration volume
of the ligand was the representation of  all frames of the ligand along the
trajectory. By the way its not quite understand for me  in one case the
measurement of the diffusion coefficient could be better than MSD which is
the measure of the random displacement of the particle itself. ( my current
taks is the examination of the ligand mobility as the rigid-body within
ligand-binding-cavity).

Also I wounder to know about some possible way to measure dynamics of the
non-covalent bonding along the trajectories.

E.g I've defined in index file all polar and aromatic residues of the
ligand-binding pocket. IS there any way to calculate all possible bonds (I
want to measure the lifetime of that bonds as well as its occurrence in
case of different ligands) between ligand and that side-chains along the
trajectory ?


James

2013/4/23 Justin Lemkul 

>
>
> On 4/23/13 10:18 AM, James Starlight wrote:
>
>> Justin,
>>
>>
>> as the example I have 2 systems consisted of receptor completed with 2
>> different ligands.
>>
>> After 100ns of production run I've realized that both of that ligands has
>> the same degree of conformational dynamics on internal degrees of freedom
>> (
>> the same RMSD as the measure of internal mobility of that compounds). But
>> the main difference was in the mobility of the smaller agonist molecule
>> (movement inside the ligand-binding pocket   in comparison to the bulkier
>> antagonist. So as consequence I've obtained  higher value of the MSD in
>> case of smaller ligand. Could the MSD be representative measure of such
>> whole-body motion of the ligand ? What advantages have the calculation of
>> the diffusion coefficient ( which could be calculated from MSD )?
>>
>>
> Maybe.  What other studies have examined similar properties, and what did
> they measure?
>
>
>  2) How I could visualize such ligand mobility ? For example for dynamics
>> on
>> internal degrees of freedom Principal components analysis could give best
>> representation of conformational mobility.
>> In case when I want to explore diffusional-behavior I should obtain
>> representation of some confrontational volume (the surface within
>> ligand-binding cavity  accessible for the ligand). What Gromac's tools
>> could be useful for that?
>>
>>
> Chapter 8 of the manual.  There may or may not be an existing Gromacs tool
> that will do the things you want.  The only way to find out is to go
> looking.
>
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
> ==**==
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[gmx-users] RMSD from the average structure

[bipin singh]

Hi all,

Please let me know whether this is the right way to calculate RMSD from the
average structure from a simulation:

g_rmsf -f traj.xtc -s average.pdb -od rmsdev.xvg


average.pdb: is the pdb file produced using -ox option of g_rmsf.

-- 
*---
Thanks and Regards,
Bipin Singh*
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