date:20111010


On 7/10/2011 9:18 PM, ITHAYARAJA wrote:

Dear Sir,

I am doing simulation work with protein-ligand complex (3 ligands). I 
modeled the protein using modeller, their ligand (two) was translated 
from the template and one them were docked by autodock 4.2. The 
protein and ligand coordinates were generated as described by the 
manual. the ligand particles were scattered out of the pocket when I 
was doing configuration (editconf -bt triclinic -f trp1.pdb -o 
trp2.pdb -d 0.85). I was using GROMOS96 43a1 force field.


You are probably seeing an artefact of 
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions


Mark



Please help me to get out of this problem.

--

Ithayaraja M,
Research Scholar,
Department of Bionformatics,
Bharathiar University,
Coimbatore 641 046,
Tamil Nadu
India




-- 
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] snap shot

2011-10-10 Thread lina

On Sat, Oct 8, 2011 at 2:21 AM, Nilesh Dhumal ndhu...@andrew.cmu.eduwrote:

 Hello,

 I have a system with 128 emi (cations) and 128 Cl (anions). I run the
 simulation for 20 ns.

 I want to save snap-shot at 5ns, 10ns, 15ns and 20ns.

trjconv  use -dt 5000


 I don't want to save snap shot for 128 ion-pairs. How can I take average
 over 128 ion pairs and save snap shot for a single ion pair.

I don't understand the average mean here?
if you wanna get the average.pdb in some time interval try g_rmsf -ox  -b -e

you may wait for some other better answers.


 Basically I want to use classical md geometry for quatum chemical
 calculation.

 I am using Gromacs 4.0.7 version.

 Thanks

 Nilesh









 --
 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

[gmx-users] Re: Question about Justin's Free Energy Tutorial

2011-10-10 Thread Fabian Casteblanco

Thank you guys for your help.   I appreciate it.

On Thu, Oct 6, 2011 at 1:05 PM, Fabian Casteblanco
fabian.castebla...@gmail.com wrote:
 Hello Justin,

 I have a question about your tutorial.  If I want to mutate one small
 group of a molecule, I would have to not provide 'couple_lambda0' and
 'couple_lambda1', correct?  I would essentially have to follow sec
 5.7.4 in the Gromacs manual and I have to actually provide all state A
 variable and all state B variables.  Gromacs would calculate the new B
 state parameters for bond lengths, angles, etc, correct?  Are there
 any other major differences to account for?

 --
 Best regards,

 Fabian F. Casteblanco
 Rutgers University --
 E:  fabian.castebla...@gmail.com




-- 
Best regards,

Fabian F. Casteblanco
Rutgers University --
Chemical Engineering PhD Student
C: +908 917 0723
E:  fabian.castebla...@gmail.com
--
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] Simulation of a crystal

Hi Valentina,

Check position_restraints (chapter 5).
These are used in standard MD during equilibration, so you can check
any tutorial protocol on how to use them.

Hope it helps,

Tsjekr

On Mon, Oct 10, 2011 at 9:22 AM, auryn_vale...@libero.it
auryn_vale...@libero.it wrote:
 Hi to everybody!!!

 I'd like to know if it is possible to simulate with gromacs a crystal
 lattice where the atoms are just kept almost fixed in their
 crystallographic structure positions and they are allowed just to vibrate
 around this positions. This is not a real MD simulation but I need it just
 to calculated radial distrubution function among the atoms in the crystal.

 Tahnk you in advance

 valentina

 --
 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




-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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] Simulation of a crystal

2011-10-10 Thread Itamar Kass

Hi,

You can use positional restrained, this will introduce some harmonic force 
which will retain the atoms to a specific position.

Itamar.

On 10/10/2011, at 6:22 PM, auryn_vale...@libero.it wrote:

 Hi to everybody!!!
 I'd like to know if it is possible to simulate with gromacs a crystal 
 lattice where the atoms are just kept almost fixed in their 
 crystallographic structure positions and they are allowed just to vibrate 
 around this positions. This is not a real MD simulation but I need it just to 
 calculated radial distrubution function among the atoms in the crystal.
 Tahnk you in advance
 valentina
 -- 
 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

-- 

In theory, there is no difference between theory and practice. But, in 
practice, there is. - Jan L.A. van de Snepscheut

===
| Itamar Kass, Ph.D.
| Postdoctoral Research Fellow
|
| Department of Biochemistry and Molecular Biology
| Building 77 Clayton Campus
| Wellington Road
| Monash University,
| Victoria 3800
| Australia
|
| Tel: +61 3 9902 9376
| Fax: +61 3 9902 9500
| E-mail:  itamar.k...@monash.edu




-- 
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] grompp error




Mark Abraham wrote:


; water topology
#include tip3p.itp


grompp is not detecting the change of [moleculetype], so you will have 
to look at the contents of that tip3p.itp and see why. I think you will 
need to #include some standard force field to get the water parameters. 
Put the #include for tip3p.itp above your [moleculetype] to get some 
different diagnostics that may be more helpful.




I think the problem is due to the fact that tip3p.itp in $GMXLIB does not 
#include the proper file in the Amber directory.  The series of #ifdefs (none of 
which can be satisfied in this topology, anyway) cover only Gromos and OPLS.


Try #include amber03.ff/tip3p.itp or something similar for whichever Amber 
force field you want to use.


-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

[gmx-users] A quick Q: How to get the history in make_ndx

2011-10-10 Thread lina

Hi,

How do I use the history input in the make_ndx prompt,

such as before I input

name 32 A2
name 33 A3

up arrow showed me:  ^[[A
Alt+up arrow showed me:  ^[[1;3A

Just curious,

Thanks,
-- 
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] g_hbond

2011-10-10 Thread Mr Bernard Ramos

Hi everyone!

I have some questions on g_hbond. According to Manual 4.5.4, hydrogen-bonds are 
counted/determined by g_hbond based on angle and distance cut-offs. The 
distance cut-off is based on the acceptor-donor distance. However, the online 
manual says that the distance is based on Hydrogen - Acceptor distance? The 
link to the online manual is as follows: 

http://manual.gromacs.org/online/g_hbond.html


I am using Gromacs 4.5.3. I found out that g_hbond does not give the correct 
counts due to a bug

http://lists.gromacs.org/pipermail/gmx-users/2011-May/061249.html


I am fairly new to using Gromacs with limited knowledge in programming. How do 
I get this bug fixed with my current version? How can I patch the fix suggested 
above?

The other question will be. Does the most recent version has the g_hbond fixed? 
I use Gromacs via Cygwin. Just in case I install the the new version, I would 
like to keep my old one. Is it ok, or do I have remove it?

Thanks.    

Bernard-- 
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] g_dipoles with net charge

2011-10-10 Thread 李浩

Dear gmx users:

I am using gms 4.07, my system contains a protein with net charge and a
plain,here I want to calculate the the angle between the dipoles of protein
and the XY plain vs. time. What should I do?

  And is this way right:

I define a positive center and a negative center, and define a vector which
point from the negative center to the positive center, and the angle between
the vector and the plain is what I want?

Or the “g_dipoles” command is exactly doing the way I mentioned before? If
so ,please tell me the details on how to get the results use this command!

 

Thanks a lot!

  Li

 

-- 
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] CMAP for alanine dipeptide in Charmm27 ff

2011-10-10 Thread César Ávila

I would like to run REMD simulations on the alanine dipeptide using the
Charmm27ff + CMAP. Still, after processing the pdb with pdb2gmx, I do not
see any entrance referring to the cmap term in the topology file. Does this
mean that Cmap won't be calculated?
-- 
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: Cloud Vs. Boinc Server?

2011-10-10 Thread Gregory Kielian

Hello All,

I am a poor, grad-student searching for a cheap/reliable way to perform
GROMACS trypsin-dynamic simulations, and I would like to hear about other's
experiences with GROMACS performance with cloud computing (i.e. Amazon's EC2
cluster compute)?

Or would it be better to try to build up a Boinc Server?

--
GK
-- 
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_in topology

2011-10-10 Thread balaji nagarajan


Dear Users ! 

I have a problem in generating the topology of the attached molecule as pdb.

earlier i have done using the same pdb for solvating the structure using spc 
and spce water box , 

there was no such error when i do for TIP4P and oplsaa force field i got the 
error 

as follows 

---
Program grompp, VERSION 4.5.3
Source code file: grompp.c, line: 523

Fatal error:
number of coordinates in coordinate file (1AKI_solv.gro, 4164)
 does not match topology (topol.top, 5527)


I used the following lines to do that 

pdb2gmx -ignh -ff oplsaa -f 1AKI.pdb -o 1AKI_processed.gro -water tip4p
editconf -f 1AKI_processed.gro -o 1AKI_newbox.gro -c -d 0.9 -bt cubic
genbox -cp 1AKI_newbox.gro -cs spc216.gro -o 1AKI_solv.gro -p topol.top
grompp -f sub.mdp -c 1AKI_solv.gro -p topol.top -o em.tpr
mdrun -v -deffnm em

in the grompp it says the error , how to solve this ,  and it comes only for 
tip4p not for other water models.

thanks in advance 
  

1AKI.pdb
Description: application/aportisdoc
-- 
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] CMAP for alanine dipeptide in Charmm27 ff

2011-10-10 Thread Jianguo Li

which gromacs version are you using? cMAP is implemented in v4.5  or later

Jianguo




From: César Ávila clav...@gmail.com
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Sunday, 9 October 2011 12:07 AM
Subject: [gmx-users] CMAP for alanine dipeptide in Charmm27 ff


I would like to run REMD simulations on the alanine dipeptide using the 
Charmm27ff + CMAP. Still, after processing the pdb with pdb2gmx, I do not see 
any entrance referring to the cmap term in the topology file. Does this mean 
that Cmap won't be calculated? 


-- 
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-- 
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_in topology




balaji nagarajan wrote:

Dear Users !

I have a problem in generating the topology of the attached molecule as pdb.

earlier i have done using the same pdb for solvating the structure using 
spc and spce water box ,


there was no such error when i do for TIP4P and oplsaa force field i got 
the error


as follows

---
Program grompp, VERSION 4.5.3
Source code file: grompp.c, line: 523

Fatal error:
number of coordinates in coordinate file (1AKI_solv.gro, 4164)
 does not match topology (topol.top, 5527)


I used the following lines to do that

pdb2gmx -ignh -ff oplsaa -f 1AKI.pdb -o 1AKI_processed.gro -water tip4p
editconf -f 1AKI_processed.gro -o 1AKI_newbox.gro -c -d 0.9 -bt cubic
genbox -cp 1AKI_newbox.gro -cs spc216.gro -o 1AKI_solv.gro -p topol.top


You told pdb2gmx to write the TIP4P topology into your .top, but then you used a 
3-point water model.  You need to solvate with tip4p.gro.


-Justin


grompp -f sub.mdp -c 1AKI_solv.gro -p topol.top -o em.tpr
mdrun -v -deffnm em

in the grompp it says the error , how to solve this ,  and it comes only 
for tip4p not for other water models.


thanks in advance



--


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

R: Re: [gmx-users] Simulation of a crystal

2011-10-10 Thread auryn_vale...@libero.it

Thank you very much...I will let you know if I can make it work ..Vale





Messaggio originale

Da: itamar.k...@monash.edu

Data: 10/10/2011 10.37

A: auryn_vale...@libero.itauryn_vale...@libero.it, Discussion list for 
GROMACS usersgmx-users@gromacs.org

Ogg: Re: [gmx-users] Simulation of a crystal



Hi,
You can use positional restrained, this will introduce some harmonic force 
which will retain the atoms to a specific position.
Itamar.
On 10/10/2011, at 6:22 PM, auryn_vale...@libero.it wrote:Hi to everybody!!!I'd 
like to know if it is possible to simulate with gromacs a crystal lattice 
where the atoms are just kept almost fixed in their crystallographic 
structure positions and they are allowed just to vibrate around this positions. 
This is not a real MD simulation but I need it just to calculated radial 
distrubution function among the atoms in the crystal. Tahnk you in advance 
valentina
-- 
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

-- 
In theory, there is no difference between theory and practice. But, in 
practice, there is. - Jan L.A. van de Snepscheut
===| Itamar Kass, Ph.D.| Postdoctoral 
Research Fellow|| Department of Biochemistry and Molecular Biology| Building 77 
Clayton Campus| Wellington Road| Monash University,| Victoria 3800| Australia|| 
Tel: +61 3 9902 9376| Fax: +61 3 9902 9500| E-mail:  
itamar.k...@monash.edu








-- 
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] snap shot


On 8/10/2011 5:21 AM, Nilesh Dhumal wrote:

Hello,

I have a system with 128 emi (cations) and 128 Cl (anions). I run the
simulation for 20 ns.

I want to save snap-shot at 5ns, 10ns, 15ns and 20ns.


So you need a suitable combination of nstxout and post-processing with 
trjconv.



I don't want to save snap shot for 128 ion-pairs. How can I take average
over 128 ion pairs and save snap shot for a single ion pair.


I don't understand what you want to do.

Mark


Basically I want to use classical md geometry for quatum chemical
calculation.

I am using Gromacs 4.0.7 version.

Thanks

Nilesh











--
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] RMSF calculations

2011-10-10 Thread Gurunath Katagi

Dear all,
I have a set of proteins(in pdb format) in which some are solved by X-ray
diffraction and some by NMR.
I have done the md simulation of these proteins using gromacs for 30ns [For
NMR structures, i have taken the first model as the starting structure]

Now, that i want to calculate the RMSF value from the simulations and
compare with the RMSF values from experimental structures [X-ray/NMR]
For the proteins with crystal structures , calculation is done using using
g_rmsf function and the comparison is done.

and  for protein from NMR structure , the RMSF values are calculated from
the simulation trajectory. But in order to compare these, how does one get
the RMSF values ? ,since
 the pdb file doesn't have the b-factors ..

Is it a good idea to use the  NMR ensembles ( usually 20 models from NMR) to
derive the RMSF  and compare these with simulation results ..?
or is there any other parameter that i can calculate from NMR models, which
is similar to RMSF ..?

Thanksin advance ..

Thanking You
Gurunath
-- 
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] Questions about dodecahedron box

2011-10-10 Thread zhenlong li

Thanks, Tsjerk.
Exactly as what you said, it was because split of molecules over
the boundary. It runs smoothly right now as I started with a dodecahedron
box.

best,
Zhenlong

On Thu, Oct 6, 2011 at 12:24 PM, Tsjerk Wassenaar tsje...@gmail.com wrote:

 Hi Zhenlong,

 I guess that some molecules got split over the boundaries during
 equilibration. You have to make them whole before changing the box.
 Better to start off with a rhombic dodecahedron though.

 Cheers,

 Tsjerk

 On Thu, Oct 6, 2011 at 6:29 PM, zhenlong li zxl1...@gmail.com wrote:
  Dear all,
  My system is based on Martini, needs a dodehedron box.
  Initially, it was minimized and equilibrated with a cubic box smoothly.
 Then
  I used the follow command to
  translate the box in to dodehedron:
   editconf -f f0.gro -bt dodecahedron  -d 2 -o vesdode.gro
  But with this change, the simulation always blows up with the message
 below.
 
  Since those atoms are most at the boundary of the box, I think it is
 because
  the overlap of boundary atoms
  with the new box type. I tried different value for -d and -box, but still
  have the same problem.
 
  Can anybody give me any hint to fix this?
 
  Thanks a lot!
  Zhenlong
 
 
 -
  Making 3D domain decomposition 7 x 4 x 3
 
  A list of missing interactions:
  Bond of  79872 missing  7
  G96Angle of  50688 missing  9
 
  Molecule type 'DPPC'
  the first 10 missing interactions, except for exclusions:
  G96Angle atoms678  global 37638 37639 37640
  Bond atoms78   global 37639 37640
  G96Angle atoms   10   11   12  global 37642 37643 37644
  Bond atoms   11   12   global 37643 37644
 
  Molecule type 'DUPC'
  the first 10 missing interactions, except for exclusions:
  G96Angle atoms   10   11   12  global 38446 38447 38448
  Bond atoms   11   12   global 38447 38448
 
  Molecule type 'DPPC'
  the first 10 missing interactions, except for exclusions:
  G96Angle atoms356  global 43395 43397 43398
  Bond atoms56   global 43397 43398
  G96Angle atoms567  global 43397 43398 43399
 
  Molecule type 'DUPC'
  the first 10 missing interactions, except for exclusions:
  G96Angle atoms678  global 45330 45331 45332
  Bond atoms78   global 45331 45332
 
  Molecule type 'DUPC'
  the first 10 missing interactions, except for exclusions:
  G96Angle atoms567  global 57173 57174 57175
  Bond atoms67   global 57174 57175
  G96Angle atoms678  global 57174 57175 57176
 
  Molecule type 'DPPC'
  the first 10 missing interactions, except for exclusions:
  G96Angle atoms678  global 63822 63823 63824
  Bond atoms78   global 63823 63824
 
 
  --
  gmx-users mailing listgmx-users@gromacs.org
  http://lists.gromacs.org/mailman/listinfo/gmx-users
  Please search the archive at
  http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
  Please don't post (un)subscribe requests to the list. Use the
  www interface or send it to gmx-users-requ...@gromacs.org.
  Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
 



 --
 Tsjerk A. Wassenaar, Ph.D.

 post-doctoral researcher
 Molecular Dynamics Group
 * Groningen Institute for Biomolecular Research and Biotechnology
 * Zernike Institute for Advanced Materials
 University of Groningen
 The Netherlands
 --
 gmx-users mailing listgmx-users@gromacs.org
 http://lists.gromacs.org/mailman/listinfo/gmx-users
 Please search the archive at
 http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
 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

[gmx-users] FEP

2011-10-10 Thread Steven Neumann

Hi Gmx Users,

Can you suggest some reading and some tutorial in calculations of binding
free energy (ligand binding) in Gromacs? ?I want to use Free Energy
Perturbation method.

Steven
-- 
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] FEP

2011-10-10 Thread mohsen ramezanpour

Hi
Please have a look at Dr.Justin tutorial page at the following link:

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html

Cheers

On Mon, Oct 10, 2011 at 12:27 PM, Steven Neumann s.neuman...@gmail.comwrote:

 Hi Gmx Users,

 Can you suggest some reading and some tutorial in calculations of binding
 free energy (ligand binding) in Gromacs? ?I want to use Free Energy
 Perturbation method.

 Steven
 --
 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

[gmx-users] FEP

2011-10-10 Thread Steven Neumann

Hi Gmx Users,

Can you suggest some reading and some tutorial in calculations of binding
free energy (ligand binding) in Gromacs? ?I want to use Free Energy
Perturbation method.

Steven
-- 
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] topology_for_3 point model

2011-10-10 Thread balaji nagarajan



Dear Users ! 

Thanks for the mail , now i fixed it 

i have a general doubt,

i saw the path of gromacs 
 /usr/local/gromacs-4.5.3/share/top

there for the three point water model only  spc216.gro is there is this common 
for 
all , ie ., spc , spc/e and tip3p.


 Date: Mon, 10 Oct 2011 07:02:04 -0400
 From: jalem...@vt.edu
 To: gmx-users@gromacs.org
 Subject: Re: [gmx-users] error_in topology
 
 
 
 balaji nagarajan wrote:
  Dear Users !
  
  I have a problem in generating the topology of the attached molecule as pdb.
  
  earlier i have done using the same pdb for solvating the structure using 
  spc and spce water box ,
  
  there was no such error when i do for TIP4P and oplsaa force field i got 
  the error
  
  as follows
  
  ---
  Program grompp, VERSION 4.5.3
  Source code file: grompp.c, line: 523
  
  Fatal error:
  number of coordinates in coordinate file (1AKI_solv.gro, 4164)
   does not match topology (topol.top, 5527)
  
  
  I used the following lines to do that
  
  pdb2gmx -ignh -ff oplsaa -f 1AKI.pdb -o 1AKI_processed.gro -water tip4p
  editconf -f 1AKI_processed.gro -o 1AKI_newbox.gro -c -d 0.9 -bt cubic
  genbox -cp 1AKI_newbox.gro -cs spc216.gro -o 1AKI_solv.gro -p topol.top
 
 You told pdb2gmx to write the TIP4P topology into your .top, but then you 
 used a 
 3-point water model.  You need to solvate with tip4p.gro.
 
 -Justin
 
  grompp -f sub.mdp -c 1AKI_solv.gro -p topol.top -o em.tpr
  mdrun -v -deffnm em
  
  in the grompp it says the error , how to solve this ,  and it comes only 
  for tip4p not for other water models.
  
  thanks in advance
  
 
 -- 
 
 
 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 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: CMAP for alanine dipeptide in Charmm27 ff

2011-10-10 Thread César Ávila

It looks like pdb2gmx does not generate an entrance for cmap terms. I added
it manually to the topology file.

2011/10/8 César Ávila clav...@gmail.com

 I would like to run REMD simulations on the alanine dipeptide using the
 Charmm27ff + CMAP. Still, after processing the pdb with pdb2gmx, I do not
 see any entrance referring to the cmap term in the topology file. Does this
 mean that Cmap won't be calculated?


-- 
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] Ligand scattered out of the protein

2011-10-10 Thread Dallas Warren

PBC issue?

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

Catch ya,

Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@monash.edu
+61 3 9903 9304
-
When the only tool you own is a hammer, every problem begins to resemble a nail.

From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On 
Behalf Of ITHAYARAJA
Sent: Friday, 7 October 2011 9:19 PM
To: gmx-users@gromacs.org
Subject: [gmx-users] Ligand scattered out of the protein

Dear Sir,

I am doing simulation work with protein-ligand complex (3 ligands). I modeled 
the protein using modeller, their ligand (two) was translated from the template 
and one them were docked by autodock 4.2. The protein and ligand coordinates 
were generated as described by the manual. the ligand particles were scattered 
out of the pocket when I was doing configuration (editconf -bt triclinic -f 
trp1.pdb -o trp2.pdb -d 0.85). I was using GROMOS96 43a1 force field.

Please help me to get out of this problem.

--

Ithayaraja M,
Research Scholar,
Department of Bionformatics,
Bharathiar University,
Coimbatore 641 046,
Tamil Nadu
India
-- 
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] g_hbond

2011-10-10 Thread Mr Bernard Ramos

Hi everyone!

I have some questions on g_hbond. According to Manual 4.5.4, hydrogen-bonds are 
counted/determined by g_hbond based on angle and distance cut-offs. The 
distance cut-off is based on the acceptor-donor distance. However, the online 
manual says that the distance is based on Hydrogen - Acceptor distance? The 
link to the online manual is as follows: 

http://manual.gromacs.org/online/g_hbond.html

I am using Gromacs 4.5.3. I found out that g_hbond does not give the correct 
counts due to a bug

http://lists.gromacs.org/pipermail/gmx-users/2011-May/061249.html

I am fairly new to using Gromacs with limited knowledge in programming. How do 
I get this bug fixed with my current version? How can I patch the fix suggested 
above?

The other question will be. Does the most recent version has the g_hbond fixed? 
I use Gromacs via Cygwin. Just in case I install the the new version, I would 
like to keep my old one. Is it ok, or do I have remove it?

Thanks.    

Bernard-- 
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] FEP




mohsen ramezanpour wrote:

Hi
Please have a look at Dr.Justin tutorial page at the following link:

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html



This tutorial is not for FEP explicitly, but may be of some use.  There is 
discussion on using the BAR algorithm for binding free energy calculations.


-Justin


Cheers

On Mon, Oct 10, 2011 at 12:27 PM, Steven Neumann s.neuman...@gmail.com 
mailto:s.neuman...@gmail.com wrote:


Hi Gmx Users,
 
Can you suggest some reading and some tutorial in calculations of

binding free energy (ligand binding) in Gromacs? ?I want to use Free
Energy Perturbation method.
 
Steven

--
gmx-users mailing listgmx-users@gromacs.org
mailto: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
mailto:gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists




--


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


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

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

Re: [gmx-users] RMSF calculations

Hi Gurunath,

Each structure in the NMR ensemble is a fit to the experimental data.
Unlike an MD trajectory, you can not assume that the set of structures
is a proper sample from the Boltzmann distribution, and therefore, the
RMSF can not be expected to correspond to the RMSF of the system. Now,
on a more qualitative level, it is likely that the parts that are less
defined in the NMR ensemble will also have larger RMSFs than the rest,
and could do for a rough comparison.

Hope it helps,

Tsjerk

On Mon, Oct 10, 2011 at 12:22 PM, Gurunath Katagi gurukat...@gmail.com wrote:
 Dear all,
 I have a set of proteins(in pdb format) in which some are solved by X-ray
 diffraction and some by NMR.
 I have done the md simulation of these proteins using gromacs for 30ns [For
 NMR structures, i have taken the first model as the starting structure]

 Now, that i want to calculate the RMSF value from the simulations and
 compare with the RMSF values from experimental structures [X-ray/NMR]
 For the proteins with crystal structures , calculation is done using using
 g_rmsf function and the comparison is done.

 and  for protein from NMR structure , the RMSF values are calculated from
 the simulation trajectory. But in order to compare these, how does one get
 the RMSF values ? ,since
  the pdb file doesn't have the b-factors ..

 Is it a good idea to use the  NMR ensembles ( usually 20 models from NMR) to
 derive the RMSF  and compare these with simulation results ..?
 or is there any other parameter that i can calculate from NMR models, which
 is similar to RMSF ..?

 Thanksin advance ..

 Thanking You
 Gurunath

 --
 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




-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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] g_hbond




Mr Bernard Ramos wrote:

Hi everyone!

I have some questions on g_hbond. According to Manual 4.5.4, 
hydrogen-bonds are counted/determined by g_hbond based on angle and 
distance cut-offs. The distance cut-off is based on the acceptor-donor 
distance. However, the online manual says that the distance is based on 
Hydrogen - Acceptor distance? The link to the online manual is as follows: 


http://manual.gromacs.org/online/g_hbond.html



It should be the donor-acceptor distance.  There was some discussion on this a 
few weeks ago.  The code


I am using Gromacs 4.5.3. I found out that g_hbond does not give the 
correct counts due to a bug


http://lists.gromacs.org/pipermail/gmx-users/2011-May/061249.html

I am fairly new to using Gromacs with limited knowledge in programming. 
How do I get this bug fixed with my current version? How can I patch the 
fix suggested above?




I wouldn't bother.  That would require cherry-picking a commit from the git 
repository.  Just upgrade to the latest version of Gromacs and it will be fixed.


The other question will be. Does the most recent version has the g_hbond 
fixed? I use Gromacs via Cygwin. Just in case I install the the new 
version, I would like to keep my old one. Is it ok, or do I have remove it?




You can maintain different versions concurrently as long as they are in discrete 
locations and you configure your environment to access the proper one (i.e. by 
sourcing the right GMXRC file).


-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] Center of mass: distance restrain for groups

2011-10-10 Thread Li, Hualin

Dear GMX users,

   I am using pull code to make a distance restrain to my proteins and 
membrane,which looks like this:



pull =   umbrella
  pull_geometry=   cylinder
 pull_vec1 =   0 0 1
 pull_r1  =   2.5
 pull_r0  =   2.5
 pull_dim =   N N Y ;# 3D

pull_start   =   yes ;# add COM distance to initial value (initial value = 
equilibrium value)
pull_ngroups =   32 ;# excluding the reference
pull_group0  =   membrane ;# the reference group - the membrane
pull_pbcatom0=   -1 ;# or -1 - important for PBC of groups larger than half 
box,
  ;# as here for membrane (see manual)
pull_group1  =   protein ;# the protein
pull_pbcatom1=   0 ;# here is no issue since protein is smaller than half 
the box
pull_rate1   =   0 ;# do not pull, just maintain distance!
pull_k1  =   800 ;# kJ mol^(-1) nm^(-2)

However, I have 32 protein to keep this local dynamic distance restrain (   
pull_geometry=   cylinder ), making the calculation goes very slowly. Is 
there any method to reduce the frequency to update the dynamic distance check 
and restrain please?

Thank you in advance.

Thanks,
Hualin --
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] Center of mass: distance restrain for groups

2011-10-10 Thread Li, Hualin

Dear GMX users,

   I am using pull code to make a distance restrain to my proteins and 
membrane,which looks like this:



pull =   umbrella
  pull_geometry=   cylinder
 pull_vec1 =   0 0 1
 pull_r1  =   2.5
 pull_r0  =   2.5
 pull_dim =   N N Y ;# 3D

pull_start   =   yes ;# add COM distance to initial value (initial value = 
equilibrium value)
pull_ngroups =   32 ;# excluding the reference
pull_group0  =   membrane ;# the reference group - the membrane
pull_pbcatom0=   -1 ;# or -1 - important for PBC of groups larger than half 
box,
  ;# as here for membrane (see manual)
pull_group1  =   protein ;# the protein
pull_pbcatom1=   0 ;# here is no issue since protein is smaller than half 
the box
pull_rate1   =   0 ;# do not pull, just maintain distance!
pull_k1  =   800 ;# kJ mol^(-1) nm^(-2)

However, I have 32 protein to keep this local dynamic distance restrain (   
pull_geometry=   cylinder ), making the calculation goes very slowly. Is 
there any method to reduce the frequency to update the dynamic distance check 
and restrain please?

Thank you in advance.

Thanks,
Hualin --
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] topology_for_3 point model




balaji nagarajan wrote:


Dear Users !

Thanks for the mail , now i fixed it

i have a general doubt,

i saw the path of gromacs
 /usr/local/gromacs-4.5.3/share/top

there for the three point water model only  spc216.gro is there is this 
common for

all , ie ., spc , spc/e and tip3p.



Please see FAQ #1 under:

http://www.gromacs.org/Documentation/FAQs#System_Preparation_and_Preprocessing

-Justin



  Date: Mon, 10 Oct 2011 07:02:04 -0400
  From: jalem...@vt.edu
  To: gmx-users@gromacs.org
  Subject: Re: [gmx-users] error_in topology
 
 
 
  balaji nagarajan wrote:
   Dear Users !
  
   I have a problem in generating the topology of the attached 
molecule as pdb.

  
   earlier i have done using the same pdb for solvating the structure 
using

   spc and spce water box ,
  
   there was no such error when i do for TIP4P and oplsaa force field 
i got

   the error
  
   as follows
  
   ---
   Program grompp, VERSION 4.5.3
   Source code file: grompp.c, line: 523
  
   Fatal error:
   number of coordinates in coordinate file (1AKI_solv.gro, 4164)
   does not match topology (topol.top, 5527)
   
  
   I used the following lines to do that
  
   pdb2gmx -ignh -ff oplsaa -f 1AKI.pdb -o 1AKI_processed.gro -water tip4p
   editconf -f 1AKI_processed.gro -o 1AKI_newbox.gro -c -d 0.9 -bt cubic
   genbox -cp 1AKI_newbox.gro -cs spc216.gro -o 1AKI_solv.gro -p topol.top
 
  You told pdb2gmx to write the TIP4P topology into your .top, but then 
you used a

  3-point water model. You need to solvate with tip4p.gro.
 
  -Justin
 
   grompp -f sub.mdp -c 1AKI_solv.gro -p topol.top -o em.tpr
   mdrun -v -deffnm em
  
   in the grompp it says the error , how to solve this , and it comes 
only

   for tip4p not for other water models.
  
   thanks in advance
  
 
  --
  
 
  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 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



--


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] Re: topology error

2011-10-10 Thread lina

On Sat, Oct 8, 2011 at 3:10 PM, ITHAYARAJA ithayar...@gmail.com wrote:

 only 59 particle variation found out of 230 ligand coordinates.

 On 8 October 2011 12:22, ITHAYARAJA ithayar...@gmail.com wrote:

 Dear Sir,


 I am actually simulating my protein with its ligand so I incorporated all
 ligand (3) coordinates to my protein .gro file and placed its .itp file
 also. I used gromas96 43a1 force field.

 I found following error when i was doing grompp for energy minimization. I
 went through FAQ and checked all but i couldn't find what exactly it was.

 So, I attached that files to you. I need your help to solve this

 Program grompp, VERSION 4.5.1
 Source code file: grompp.c, line: 377

 Fatal error:
 number of coordinates in coordinate file (GR_b4ion.gro, 66074)
  does not match topology (GR.top, 66015)


I used to count the atom numbers in .gro file and manually modify the
topology to make them match.




 --
 **
 Ithayaraja M,
 Research Scholar,
 Department of Bionformatics,
 Bharathiar University,
 Coimbatore 641 046,
 Tamil Nadu
 India




 --
 **
 Ithayaraja M,
 Research Scholar,
 Department of Bionformatics,
 Bharathiar University,
 Coimbatore 641 046,
 Tamil Nadu
 India

 --
 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] g_hbond




Justin A. Lemkul wrote:



Mr Bernard Ramos wrote:

Hi everyone!

I have some questions on g_hbond. According to Manual 4.5.4, 
hydrogen-bonds are counted/determined by g_hbond based on angle and 
distance cut-offs. The distance cut-off is based on the acceptor-donor 
distance. However, the online manual says that the distance is based 
on Hydrogen - Acceptor distance? The link to the online manual is as 
follows:

http://manual.gromacs.org/online/g_hbond.html



It should be the donor-acceptor distance.  There was some discussion on 
this a few weeks ago.  The code




Oops, forgot to finish that thought.  Someone came into my office...

Where I was going was that the code is very convoluted and I honestly can't 
follow it, so hopefully a developer can confirm the proper action so the 
documentation can be updated.


-Justin

I am using Gromacs 4.5.3. I found out that g_hbond does not give the 
correct counts due to a bug


http://lists.gromacs.org/pipermail/gmx-users/2011-May/061249.html

I am fairly new to using Gromacs with limited knowledge in 
programming. How do I get this bug fixed with my current version? How 
can I patch the fix suggested above?




I wouldn't bother.  That would require cherry-picking a commit from the 
git repository.  Just upgrade to the latest version of Gromacs and it 
will be fixed.


The other question will be. Does the most recent version has the 
g_hbond fixed? I use Gromacs via Cygwin. Just in case I install the 
the new version, I would like to keep my old one. Is it ok, or do I 
have remove it?




You can maintain different versions concurrently as long as they are in 
discrete locations and you configure your environment to access the 
proper one (i.e. by sourcing the right GMXRC file).


-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] FEP

2011-10-10 Thread Steven Neumann

Thank you guys! So, is there any tutorial in Gromacs for calculating free
energy of ligand binding using FEP?

Steven

On Mon, Oct 10, 2011 at 2:02 PM, Justin A. Lemkul jalem...@vt.edu wrote:



 mohsen ramezanpour wrote:

 Hi
 Please have a look at Dr.Justin tutorial page at the following link:

 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin/**
 gmx-tutorials/index.htmlhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html


 This tutorial is not for FEP explicitly, but may be of some use.  There is
 discussion on using the BAR algorithm for binding free energy calculations.

 -Justin

 Cheers


 On Mon, Oct 10, 2011 at 12:27 PM, Steven Neumann 
 s.neuman...@gmail.commailto:
 s.neuman...@gmail.com** wrote:

Hi Gmx Users,
 Can you suggest some reading and some tutorial in calculations of
binding free energy (ligand binding) in Gromacs? ?I want to use Free
Energy Perturbation method.
 Steven
--
gmx-users mailing listgmx-users@gromacs.org
mailto:gmx-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
mailto:gmx-users-request@**gromacs.orggmx-users-requ...@gromacs.org.


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



 --
 ==**==

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

Re: [gmx-users] FEP




Steven Neumann wrote:
Thank you guys! So, is there any tutorial in Gromacs for calculating 
free energy of ligand binding using FEP?
 


TI or BAR are better methods for calculating binding free energies, I would 
think.  FEP is best for mutating between different species.


-Justin


Steven

On Mon, Oct 10, 2011 at 2:02 PM, Justin A. Lemkul jalem...@vt.edu 
mailto:jalem...@vt.edu wrote:




mohsen ramezanpour wrote:

Hi
Please have a look at Dr.Justin tutorial page at the following link:


http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin/__gmx-tutorials/index.html

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html


This tutorial is not for FEP explicitly, but may be of some use.
 There is discussion on using the BAR algorithm for binding free
energy calculations.

-Justin

Cheers


On Mon, Oct 10, 2011 at 12:27 PM, Steven Neumann
s.neuman...@gmail.com mailto:s.neuman...@gmail.com
mailto:s.neuman...@gmail.com mailto:s.neuman...@gmail.com__
wrote:

   Hi Gmx Users,
Can you suggest some reading and some tutorial in
calculations of
   binding free energy (ligand binding) in Gromacs? ?I want to
use Free
   Energy Perturbation method.
Steven
   --
   gmx-users mailing listgmx-users@gromacs.org
mailto:gmx-users@gromacs.org
   mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org

   http://lists.gromacs.org/__mailman/listinfo/gmx-users
http://lists.gromacs.org/mailman/listinfo/gmx-users
   Please search the archive at
   http://www.gromacs.org/__Support/Mailing_Lists/Search
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
mailto:gmx-users-requ...@gromacs.org
   mailto:gmx-users-request@__gromacs.org
mailto:gmx-users-requ...@gromacs.org.

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



-- 
==__==


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu http://vt.edu/ | (540) 231-9080
tel:%28540%29%20231-9080
http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

==__==

-- 
gmx-users mailing listgmx-users@gromacs.org

mailto:gmx-users@gromacs.org
http://lists.gromacs.org/__mailman/listinfo/gmx-users
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/__Support/Mailing_Lists/Search
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
mailto:gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists
http://www.gromacs.org/Support/Mailing_Lists




--


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


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

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

[gmx-users] How to obtain structures with large RMSD?

Hi, all,

I am trying to use Gromacs to obtain structural ensembles around native
structures (PDB structures).
However the simulated structures are always very close to the initial one,
with RMSD  0.2.
I am wondering how to obtain large-RMSD structures? Thanks.

-- 
Best,
Liang Liu
-- 
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] How to obtain structures with large RMSD?




Liu, Liang wrote:

Hi, all,

I am trying to use Gromacs to obtain structural ensembles around native 
structures (PDB structures).
However the simulated structures are always very close to the initial 
one, with RMSD  0.2.

I am wondering how to obtain large-RMSD structures? Thanks.



Large RMSD values would indicate non-native structures, which doesn't sound like 
what you're looking for.  If your goal is simply enhanced sampling, try REMD.


-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] How to obtain structures with large RMSD?

Thanks.

Will the constrain help?

On Mon, Oct 10, 2011 at 10:06 AM, Justin A. Lemkul jalem...@vt.edu wrote:



 Liu, Liang wrote:

 Hi, all,

 I am trying to use Gromacs to obtain structural ensembles around native
 structures (PDB structures).
 However the simulated structures are always very close to the initial one,
 with RMSD  0.2.
 I am wondering how to obtain large-RMSD structures? Thanks.


 Large RMSD values would indicate non-native structures, which doesn't sound
 like what you're looking for.  If your goal is simply enhanced sampling, try
 REMD.

 -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




-- 
Best,
Liang Liu
-- 
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] How to obtain structures with large RMSD?




Liu, Liang wrote:

Thanks.

Will the constrain help?



Bond constraints?  Well, in general, they're useful, and likely necessary at 
high temperature to keep your system stable.  Please be more specific.


-Justin

On Mon, Oct 10, 2011 at 10:06 AM, Justin A. Lemkul jalem...@vt.edu 
mailto:jalem...@vt.edu wrote:




Liu, Liang wrote:

Hi, all,

I am trying to use Gromacs to obtain structural ensembles around
native structures (PDB structures).
However the simulated structures are always very close to the
initial one, with RMSD  0.2.
I am wondering how to obtain large-RMSD structures? Thanks.


Large RMSD values would indicate non-native structures, which
doesn't sound like what you're looking for.  If your goal is simply
enhanced sampling, try REMD.

-Justin

-- 
==__==


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu http://vt.edu | (540) 231-9080
tel:%28540%29%20231-9080
http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

==__==
-- 
gmx-users mailing listgmx-users@gromacs.org

mailto:gmx-users@gromacs.org
http://lists.gromacs.org/__mailman/listinfo/gmx-users
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/__Support/Mailing_Lists/Search
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
mailto:gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists
http://www.gromacs.org/Support/Mailing_Lists




--
Best,
Liang Liu


--


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] How to obtain structures with large RMSD?

Hey Justin,
 Large RMSD values would indicate non-native structures, which doesn't sound
 like what you're looking for.  If your goal is simply enhanced sampling, try
 REMD.

I think this is put too boldly. There are plenty of examples where
pairs from native ensembles have large RMSD: e.g., proteins in
alternative conformational states and intrinsically disordered
proteins. The RMSD doesn't say anything about 'correctness' or
'nativeness', only about (dis)similarity.
The RMSD distribution widens with denaturation, which might actually
be what was meant. In that case, large(r) RMSD values can be obtained
by raising the temperature, possibly as part of an extended sampling
scheme, such as REMD.

Cheers,

Tsjerk


-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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: A quick Q: How to get the history in make_ndx

2011-10-10 Thread Dr. Vitaly V. Chaban


 How do I use the history input in the make_ndx prompt,

 such as before I input

 name 32 A2
 name 33 A3

 up arrow showed me:  ^[[A
 Alt+up arrow showed me:  ^[[1;3A


Such behavior is not programmed. You are welcome to add the necessary
part of the code. CTRL+C/V solves the problem.


-- 
Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept.
Univ. Rochester, Rochester, New York 14627-0216
THE UNITED STATES OF AMERICA
-- 
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] How to obtain structures with large RMSD?




Tsjerk Wassenaar wrote:

Hey Justin,

Large RMSD values would indicate non-native structures, which doesn't sound
like what you're looking for.  If your goal is simply enhanced sampling, try
REMD.


I think this is put too boldly. There are plenty of examples where
pairs from native ensembles have large RMSD: e.g., proteins in
alternative conformational states and intrinsically disordered
proteins. The RMSD doesn't say anything about 'correctness' or
'nativeness', only about (dis)similarity.


Quite right.  I guess I just took the OP's stated desire for sampling around the 
native structure, which considered the PDB structure itself to be native. 
Thanks for the clarification; indeed an important point.


-Justin


The RMSD distribution widens with denaturation, which might actually
be what was meant. In that case, large(r) RMSD values can be obtained
by raising the temperature, possibly as part of an extended sampling
scheme, such as REMD.

Cheers,

Tsjerk




--


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] How to obtain structures with large RMSD?

How's position restraint? If the force constant is reduced (reduce the
number in posre.itp ?), the simulation will lead to more flexible structure?

On Mon, Oct 10, 2011 at 10:20 AM, Justin A. Lemkul jalem...@vt.edu wrote:



 Liu, Liang wrote:

 Thanks.

 Will the constrain help?


 Bond constraints?  Well, in general, they're useful, and likely necessary
 at high temperature to keep your system stable.  Please be more specific.

 -Justin

  On Mon, Oct 10, 2011 at 10:06 AM, Justin A. Lemkul jalem...@vt.edumailto:
 jalem...@vt.edu wrote:



Liu, Liang wrote:

Hi, all,

I am trying to use Gromacs to obtain structural ensembles around
native structures (PDB structures).
However the simulated structures are always very close to the
initial one, with RMSD  0.2.
I am wondering how to obtain large-RMSD structures? Thanks.


Large RMSD values would indicate non-native structures, which
doesn't sound like what you're looking for.  If your goal is simply
enhanced sampling, try REMD.

-Justin

-- ==**__==


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu http://vt.edu | (540) 231-9080
tel:%28540%29%20231-9080

 http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justinhttp://vt.edu/Pages/Personal/justin

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

==**__==

-- gmx-users mailing listgmx-users@gromacs.org
mailto:gmx-users@gromacs.org

 http://lists.gromacs.org/__**mailman/listinfo/gmx-usershttp://lists.gromacs.org/__mailman/listinfo/gmx-users


 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/Search


 http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://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
mailto:gmx-users-request@**gromacs.orggmx-users-requ...@gromacs.org
 .
Can't post? Read 
 http://www.gromacs.org/__**Support/Mailing_Listshttp://www.gromacs.org/__Support/Mailing_Lists


 http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists
 




 --
 Best,
 Liang Liu


 --
 ==**==

 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




-- 
Best,
Liang Liu
-- 
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] How to obtain structures with large RMSD?

Hi Liang Liu,

You will never get broader sampling by adding restraints. If you want
to have broader sampling, raise the temperature or add denaturants.
But also ask yourself the question if what you think you want is what
you should be wanting. What is the actual question you're trying to
solve?

Cheers,

Tsjerk

On Mon, Oct 10, 2011 at 5:32 PM, Liu, Liang liu4...@gmail.com wrote:
 How's position restraint? If the force constant is reduced (reduce the
 number in posre.itp ?), the simulation will lead to more flexible structure?

 On Mon, Oct 10, 2011 at 10:20 AM, Justin A. Lemkul jalem...@vt.edu wrote:


 Liu, Liang wrote:

 Thanks.

 Will the constrain help?


 Bond constraints?  Well, in general, they're useful, and likely necessary
 at high temperature to keep your system stable.  Please be more specific.

 -Justin

 On Mon, Oct 10, 2011 at 10:06 AM, Justin A. Lemkul jalem...@vt.edu
 mailto:jalem...@vt.edu wrote:



    Liu, Liang wrote:

        Hi, all,

        I am trying to use Gromacs to obtain structural ensembles around
        native structures (PDB structures).
        However the simulated structures are always very close to the
        initial one, with RMSD  0.2.
        I am wondering how to obtain large-RMSD structures? Thanks.


    Large RMSD values would indicate non-native structures, which
    doesn't sound like what you're looking for.  If your goal is simply
    enhanced sampling, try REMD.

    -Justin

    --     ==__==

    Justin A. Lemkul
    Ph.D. Candidate
    ICTAS Doctoral Scholar
    MILES-IGERT Trainee
    Department of Biochemistry
    Virginia Tech
    Blacksburg, VA
    jalemkul[at]vt.edu http://vt.edu | (540) 231-9080
    tel:%28540%29%20231-9080
    http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
    http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

    ==__==
    --     gmx-users mailing list    gmx-users@gromacs.org
    mailto:gmx-users@gromacs.org
    http://lists.gromacs.org/__mailman/listinfo/gmx-users
    http://lists.gromacs.org/mailman/listinfo/gmx-users
    Please search the archive at
    http://www.gromacs.org/__Support/Mailing_Lists/Search
    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
    mailto:gmx-users-requ...@gromacs.org.
    Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists
    http://www.gromacs.org/Support/Mailing_Lists




 --
 Best,
 Liang Liu

 --
 

 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 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



 --
 Best,
 Liang Liu

 --
 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




-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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] How to obtain structures with large RMSD?




Liu, Liang wrote:
How's position restraint? If the force constant is reduced (reduce the 
number in posre.itp ?), the simulation will lead to more flexible structure?




Position restraints are inherent inhibition to structural sampling.  Their 
intent is to prevent the protein (or whatever restrained molecule) from changing 
too much.  Of course, it can change since it's only a harmonic potential, but if 
you're looking for better sampling then I would turn off any form of position 
restraints.


-Justin

On Mon, Oct 10, 2011 at 10:20 AM, Justin A. Lemkul jalem...@vt.edu 
mailto:jalem...@vt.edu wrote:




Liu, Liang wrote:

Thanks.

Will the constrain help?


Bond constraints?  Well, in general, they're useful, and likely
necessary at high temperature to keep your system stable.  Please be
more specific.

-Justin

On Mon, Oct 10, 2011 at 10:06 AM, Justin A. Lemkul
jalem...@vt.edu mailto:jalem...@vt.edu
mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote:



   Liu, Liang wrote:

   Hi, all,

   I am trying to use Gromacs to obtain structural ensembles
around
   native structures (PDB structures).
   However the simulated structures are always very close to the
   initial one, with RMSD  0.2.
   I am wondering how to obtain large-RMSD structures? Thanks.


   Large RMSD values would indicate non-native structures, which
   doesn't sound like what you're looking for.  If your goal is
simply
   enhanced sampling, try REMD.

   -Justin

   -- ====


   Justin A. Lemkul
   Ph.D. Candidate
   ICTAS Doctoral Scholar
   MILES-IGERT Trainee
   Department of Biochemistry
   Virginia Tech
   Blacksburg, VA
   jalemkul[at]vt.edu http://vt.edu http://vt.edu | (540)
231-9080 tel:%28540%29%20231-9080
   tel:%28540%29%20231-9080
   http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
http://vt.edu/Pages/Personal/justin
   http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

   ====

   -- gmx-users mailing listgmx-users@gromacs.org
mailto:gmx-users@gromacs.org
   mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org
   http://lists.gromacs.org/mailman/listinfo/gmx-users
http://lists.gromacs.org/__mailman/listinfo/gmx-users

   http://lists.gromacs.org/__mailman/listinfo/gmx-users
http://lists.gromacs.org/mailman/listinfo/gmx-users
   Please search the archive at
   http://www.gromacs.org/Support/Mailing_Lists/Search
http://www.gromacs.org/__Support/Mailing_Lists/Search

   http://www.gromacs.org/__Support/Mailing_Lists/Search
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
mailto:gmx-users-requ...@gromacs.org
   mailto:gmx-users-request@__gromacs.org
mailto:gmx-users-requ...@gromacs.org.
   Can't post? Read
http://www.gromacs.org/Support/Mailing_Lists
http://www.gromacs.org/__Support/Mailing_Lists

   http://www.gromacs.org/__Support/Mailing_Lists
http://www.gromacs.org/Support/Mailing_Lists




-- 
Best,

Liang Liu


-- 
==__==


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu http://vt.edu | (540) 231-9080
tel:%28540%29%20231-9080
http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

==__==
-- 
gmx-users mailing listgmx-users@gromacs.org

mailto:gmx-users@gromacs.org
http://lists.gromacs.org/__mailman/listinfo/gmx-users
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/__Support/Mailing_Lists/Search
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
mailto:gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists
http://www.gromacs.org/Support/Mailing_Lists




--
Best,
Liang Liu


--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of

Re: [gmx-users] How to obtain structures with large RMSD?

Well, I am only trying to get structures with some of them far from the
initial structure (large RMSD) and some of them close to the initial one...

On Mon, Oct 10, 2011 at 10:37 AM, Tsjerk Wassenaar tsje...@gmail.comwrote:

 Hi Liang Liu,

 You will never get broader sampling by adding restraints. If you want
 to have broader sampling, raise the temperature or add denaturants.
 But also ask yourself the question if what you think you want is what
 you should be wanting. What is the actual question you're trying to
 solve?

 Cheers,

 Tsjerk

 On Mon, Oct 10, 2011 at 5:32 PM, Liu, Liang liu4...@gmail.com wrote:
  How's position restraint? If the force constant is reduced (reduce the
  number in posre.itp ?), the simulation will lead to more flexible
 structure?
 
  On Mon, Oct 10, 2011 at 10:20 AM, Justin A. Lemkul jalem...@vt.edu
 wrote:
 
 
  Liu, Liang wrote:
 
  Thanks.
 
  Will the constrain help?
 
 
  Bond constraints?  Well, in general, they're useful, and likely
 necessary
  at high temperature to keep your system stable.  Please be more
 specific.
 
  -Justin
 
  On Mon, Oct 10, 2011 at 10:06 AM, Justin A. Lemkul jalem...@vt.edu
  mailto:jalem...@vt.edu wrote:
 
 
 
 Liu, Liang wrote:
 
 Hi, all,
 
 I am trying to use Gromacs to obtain structural ensembles around
 native structures (PDB structures).
 However the simulated structures are always very close to the
 initial one, with RMSD  0.2.
 I am wondering how to obtain large-RMSD structures? Thanks.
 
 
 Large RMSD values would indicate non-native structures, which
 doesn't sound like what you're looking for.  If your goal is simply
 enhanced sampling, try REMD.
 
 -Justin
 
 -- ==__==
 
 Justin A. Lemkul
 Ph.D. Candidate
 ICTAS Doctoral Scholar
 MILES-IGERT Trainee
 Department of Biochemistry
 Virginia Tech
 Blacksburg, VA
 jalemkul[at]vt.edu http://vt.edu | (540) 231-9080
 tel:%28540%29%20231-9080
 http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
 
 ==__==
 -- gmx-users mailing listgmx-users@gromacs.org
 mailto:gmx-users@gromacs.org
 http://lists.gromacs.org/__mailman/listinfo/gmx-users
 http://lists.gromacs.org/mailman/listinfo/gmx-users
 Please search the archive at
 http://www.gromacs.org/__Support/Mailing_Lists/Search
 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
 mailto:gmx-users-requ...@gromacs.org.
 Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists
 http://www.gromacs.org/Support/Mailing_Lists
 
 
 
 
  --
  Best,
  Liang Liu
 
  --
  
 
  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
 
 
 
  --
  Best,
  Liang Liu
 
  --
  gmx-users mailing listgmx-users@gromacs.org
  http://lists.gromacs.org/mailman/listinfo/gmx-users
  Please search the archive at
  http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
  Please don't post (un)subscribe requests to the list. Use the
  www interface or send it to gmx-users-requ...@gromacs.org.
  Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
 



 --
 Tsjerk A. Wassenaar, Ph.D.

 post-doctoral researcher
 Molecular Dynamics Group
 * Groningen Institute for Biomolecular Research and Biotechnology
 * Zernike Institute for Advanced Materials
 University of Groningen
 The Netherlands
 --
 gmx-users mailing listgmx-users@gromacs.org
 http://lists.gromacs.org/mailman/listinfo/gmx-users
 Please search the archive at
 http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
 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




-- 
Best,
Liang Liu
-- 
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

Re: [gmx-users] How to obtain structures with large RMSD?

Well, the thing is even I turn off the position restraint and raise the
temperature to 600k, the RMSD I can obtained is only about 0.3 for a RNA
hairpin.
-- 
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] FEP

2011-10-10 Thread Michael Shirts

FEP is a poorly defined term.  It can either mean 1) making small
changes 'alchemical' changes in the molecules and computing the free
energies by any method (BAR, TI, etc), or 2) it can mean specifically
computing the free energies by exponentially averaging the potential
energy differences.  Basically, using the exponential averaging
formula is a bad idea -- if you have code that only uses that method,
you can get decent results out if you are careful, but TI, BAR, and
MBAR are all better choices.

On Mon, Oct 10, 2011 at 10:58 AM, Justin A. Lemkul jalem...@vt.edu wrote:


 Steven Neumann wrote:

 Thank you guys! So, is there any tutorial in Gromacs for calculating free
 energy of ligand binding using FEP?


 TI or BAR are better methods for calculating binding free energies, I would
 think.  FEP is best for mutating between different species.

 -Justin

 Steven

 On Mon, Oct 10, 2011 at 2:02 PM, Justin A. Lemkul jalem...@vt.edu
 mailto:jalem...@vt.edu wrote:



    mohsen ramezanpour wrote:

        Hi
        Please have a look at Dr.Justin tutorial page at the following
 link:


  http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin/__gmx-tutorials/index.html

  http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html


    This tutorial is not for FEP explicitly, but may be of some use.
     There is discussion on using the BAR algorithm for binding free
    energy calculations.

    -Justin

        Cheers


        On Mon, Oct 10, 2011 at 12:27 PM, Steven Neumann
        s.neuman...@gmail.com mailto:s.neuman...@gmail.com
        mailto:s.neuman...@gmail.com mailto:s.neuman...@gmail.com__
        wrote:

           Hi Gmx Users,
                Can you suggest some reading and some tutorial in
        calculations of
           binding free energy (ligand binding) in Gromacs? ?I want to
        use Free
           Energy Perturbation method.
                Steven
           --
           gmx-users mailing list    gmx-users@gromacs.org
        mailto:gmx-users@gromacs.org
           mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org

           http://lists.gromacs.org/__mailman/listinfo/gmx-users
        http://lists.gromacs.org/mailman/listinfo/gmx-users
           Please search the archive at
           http://www.gromacs.org/__Support/Mailing_Lists/Search
        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
        mailto:gmx-users-requ...@gromacs.org
           mailto:gmx-users-request@__gromacs.org
        mailto:gmx-users-requ...@gromacs.org.

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



    --     ==__==

    Justin A. Lemkul
    Ph.D. Candidate
    ICTAS Doctoral Scholar
    MILES-IGERT Trainee
    Department of Biochemistry
    Virginia Tech
    Blacksburg, VA
    jalemkul[at]vt.edu http://vt.edu/ | (540) 231-9080
    tel:%28540%29%20231-9080
    http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
    http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

    ==__==

    --     gmx-users mailing list    gmx-users@gromacs.org
    mailto:gmx-users@gromacs.org
    http://lists.gromacs.org/__mailman/listinfo/gmx-users
    http://lists.gromacs.org/mailman/listinfo/gmx-users
    Please search the archive at
    http://www.gromacs.org/__Support/Mailing_Lists/Search
    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
    mailto:gmx-users-requ...@gromacs.org.
    Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists
    http://www.gromacs.org/Support/Mailing_Lists



 --
 

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

 
 --
 gmx-users mailing 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

--
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] Conference Frontiers in Biomolecular Simulation

2011-10-10 Thread Rainer Boeckmann

We are proud to announce the 495. Wilhelm und Else Heraeus-Seminar
Frontiers in Biomolecular Simulation to take place on Jan. 22.-25. 2012
at the Physikzentrum Bad Honnef in Germany. The conference is sponsored by
the Heraeus-Foundation, Germany's premier private organisation for the
advancement of physics.

The conference will deal with the topics of Coarse Grained Models and
Methods, Simulating Membranes and Membrane Proteins, Large Scale Quantum
Processes and Multiscale and Large Scale Biomolecular Simulation. We are
happy to announce that more than 20 distinguished international speakers
are committed to make this an intimate, highly productive meeting.

Please refer to:

http://www.rz.uni-karlsruhe.de/~cd186/

for more information.

At the moment, we are encouraging scientists to apply for ca. 30 attendee
slots at the meeting which will be filled until Oct. 30th. The conference
is free to attend and includes foodlodging, participants only have to
cover their own travel costs. We expect slots to fill up very quickly, so
please register early. We especially encourage junior group leaders and
scientists beginning work in the field of Biomolecular Simulation to
attend and present posters on their recent work.

Kind Regards,

Dr. Thomas Steinbrecher

also on behalf of my Co-organizers:

Marcus Elstner, Rainer Boeckmann and Christine Peter

__
Prof. Dr. Rainer Böckmann
Computational Biology
Universität Erlangen-Nürnberg
Staudtstr. 5
91058 Erlangen
Phone:++49 +9131 85-25409 FAX: ++49 +9131 85-25410
E-Mail: rainer.boeckm...@biologie.uni-erlangen.de
http://www.biotechnik.nat.uni-erlangen.de/research/boeckmann/
___


-- 
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] using gromacs with an specific GCC

2011-10-10 Thread Nathalia Garces

Good morning,

I'm trying to use Scientific Linux 5.5 to run Gromacs 4.5.4. The problem is
that the default version of gcc in this distribution is 4.1, which is broken
for Gromacs!!
I can install a newer version of gcc in compatible mode with gcc 4.1, but
the last one will still be the default.
Now, my problem is that I don't know how to specify to Gromacs to use the
newer version. I've seen that you can specify which gcc to use while you
configure the program, but I found no information of how to specify which
compiler to use while running a MD simulation??.. I mean when using mdrun
command or even while using every command in Gromacs.


Thank you for four answer

Nathalia
-- 
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] Virtual Sites in a polymer backbone

2011-10-10 Thread Broadbent, Richard


I wish to keep certain parts of the backbone of my polymer rigid and planar,
as my primary interest is in the long length and timescale motion of the
polymer. 

I am attempting to utilise virtual sites as a means to keep aromatic groups
rigid and planar. My intention is to replace groups such as phenyl rings and
connected 5 and 6 member rings (similar to Phthalimide) with 3 reference
sites, then virtualise all the atomic sites. I'm going to use standard type
3 virtual sites and planned on constraining the relative positions of the 3
reference points. 

My plan is to pick sites such that the 3 eigenvalues of the moment of
inertia tensor, the centre of mass, and the total mass of the system are
conserved. As the system is two dimensional this amounts to a total of 6
non-linear equations for 9 variables which requires either additional
constraints or a physically motivated guess to solve.

I've searched the mailing list but have been unable to find any previous
attempts at this. I was wondering if anyone knew of a reference where this
had been attempted or if there had been any previous discussions about an
approach similar to this?

I am also very open to alternative approaches to holding these groups
planar.

Many thanks,

Richard

--
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] Virtual Sites in a polymer backbone




Broadbent, Richard wrote:

I wish to keep certain parts of the backbone of my polymer rigid and planar,
as my primary interest is in the long length and timescale motion of the
polymer. 


I am attempting to utilise virtual sites as a means to keep aromatic groups
rigid and planar. My intention is to replace groups such as phenyl rings and
connected 5 and 6 member rings (similar to Phthalimide) with 3 reference
sites, then virtualise all the atomic sites. I'm going to use standard type
3 virtual sites and planned on constraining the relative positions of the 3
reference points. 


My plan is to pick sites such that the 3 eigenvalues of the moment of
inertia tensor, the centre of mass, and the total mass of the system are
conserved. As the system is two dimensional this amounts to a total of 6
non-linear equations for 9 variables which requires either additional
constraints or a physically motivated guess to solve.

I've searched the mailing list but have been unable to find any previous
attempts at this. I was wondering if anyone knew of a reference where this
had been attempted or if there had been any previous discussions about an
approach similar to this?

I am also very open to alternative approaches to holding these groups
planar.



Any particular reason why improper dihedrals would not be suitable?  They are 
significantly easier to implement.


-Justin


Many thanks,

Richard



--


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] using gromacs with an specific GCC




Nathalia Garces wrote:

Good morning,

I'm trying to use Scientific Linux 5.5 to run Gromacs 4.5.4. The problem 
is that the default version of gcc in this distribution is 4.1, which is 
broken for Gromacs!!
I can install a newer version of gcc in compatible mode with gcc 4.1, 
but the last one will still be the default.
Now, my problem is that I don't know how to specify to Gromacs to use 
the newer version. I've seen that you can specify which gcc to use while 
you configure the program, but I found no information of how to specify 
which compiler to use while running a MD simulation??.. I mean when 
using mdrun command or even while using every command in Gromacs.




You do not need to specify your gcc after the code is built.

-Justin




Thank you for four answer

Nathalia



--


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] snap shot

2011-10-10 Thread Nilesh Dhumal

Hello,

How can I save the coordinates  (in pdb or xyz format) for a particular
snap shot.

Nilesh

On Sat, October 8, 2011 10:06 am, lina wrote:
 On Sat, Oct 8, 2011 at 2:21 AM, Nilesh Dhumal
 ndhu...@andrew.cmu.eduwrote:


 Hello,


 I have a system with 128 emi (cations) and 128 Cl (anions). I run the
 simulation for 20 ns.

 I want to save snap-shot at 5ns, 10ns, 15ns and 20ns.


 trjconv  use -dt 5000


 I don't want to save snap shot for 128 ion-pairs. How can I take
 average over 128 ion pairs and save snap shot for a single ion pair.

 I don't understand the average mean here?
 if you wanna get the average.pdb in some time interval try g_rmsf -ox  -b
 -e


 you may wait for some other better answers.


 Basically I want to use classical md geometry for quatum chemical
 calculation.

 I am using Gromacs 4.0.7 version.


 Thanks


 Nilesh










 --
 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


-- 
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] snap shot




Nilesh Dhumal wrote:

Hello,

How can I save the coordinates  (in pdb or xyz format) for a particular
snap shot.



trjconv -dump

-Justin


Nilesh

On Sat, October 8, 2011 10:06 am, lina wrote:

On Sat, Oct 8, 2011 at 2:21 AM, Nilesh Dhumal
ndhu...@andrew.cmu.eduwrote:



Hello,


I have a system with 128 emi (cations) and 128 Cl (anions). I run the
simulation for 20 ns.

I want to save snap-shot at 5ns, 10ns, 15ns and 20ns.



trjconv  use -dt 5000


I don't want to save snap shot for 128 ion-pairs. How can I take
average over 128 ion pairs and save snap shot for a single ion pair.


I don't understand the average mean here?
if you wanna get the average.pdb in some time interval try g_rmsf -ox  -b
-e


you may wait for some other better answers.



Basically I want to use classical md geometry for quatum chemical
calculation.

I am using Gromacs 4.0.7 version.


Thanks


Nilesh










--
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





--


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] CMAP for alanine dipeptide in Charmm27 ff

2011-10-10 Thread César Ávila

v4.5.4
As I commented above, I had to manually add an entrance for the cmap terms
in the topology file as pdb2gmx would not generate them for the alanine
dipeptide. There seems to be no problem for larger peptides.
Cheers
Cesar

2011/10/10 Jianguo Li ljg...@yahoo.com.sg

 which gromacs version are you using? cMAP is implemented in v4.5  or later
 Jianguo

 --
 *From:* César Ávila clav...@gmail.com
 *To:* Discussion list for GROMACS users gmx-users@gromacs.org
 *Sent:* Sunday, 9 October 2011 12:07 AM
 *Subject:* [gmx-users] CMAP for alanine dipeptide in Charmm27 ff

 I would like to run REMD simulations on the alanine dipeptide using the
 Charmm27ff + CMAP. Still, after processing the pdb with pdb2gmx, I do not
 see any entrance referring to the cmap term in the topology file. Does this
 mean that Cmap won't be calculated?


 --
 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

-- 
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] Virtual Sites in a polymer backbone

2011-10-10 Thread Broadbent, Richard

 
 Any particular reason why improper dihedrals would not be suitable?  They are
 significantly easier to implement.
Yes the force field parameters for the molecule are not known and I am
therefore fitting the parameters to Density Functional Theory. If I allow
the units to move out of plane even slightly their will be additional
parameters to fit which will make the problem unfeasibly computationally
expensive.

Thank you for the suggestion,

Richard

--
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] How to obtain structures with large RMSD?

2011-10-10 Thread KS Rotondi


you either

A) Have not been sampling long enough

or

B) Just might have your answer...

On Oct 10, 2011, at 11:46 AM, Liu, Liang wrote:

Well, the thing is even I turn off the position restraint and raise  
the temperature to 600k, the RMSD I can obtained is only about 0.3  
for a RNA hairpin. --

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

[gmx-users] problem_with_rewritting_pdb

2011-10-10 Thread balaji nagarajan


Dear Users ! 

I have minimized the attached file using the gromacs43a1 and oplsaa force field 
using spc water molecules 

I have used the following script for generating topology . 
i minimized for 2000 steps , my doubt is when i rewrite the minimized pdb , in 
case of oplsaa 
i was able to get all atoms , but in the case of the gromacs43a1 i am not 
getting the hydrogen atoms of the protein , 

how to solve this 

here is the steps which i have used 

---
pdb2gmx -ignh -ff oplsaa -f 1AKI.pdb -o 1AKI_processed.gro -water spc
editconf -f 1AKI_processed.gro -o 1AKI_newbox.gro -c -d 0.9 -bt cubic
genbox -cp 1AKI_newbox.gro -cs spc216.gro -o 1AKI_solv.gro -p topol.top
grompp -f minim.mdp -c 1AKI_solv.gro -p topol.top -o em.tpr
mdrun -v -deffnm em
trjconv -f em.trr -o min.pdb -s em.tpr ( in this i gave the option 0 for the 
total system)
--
the minim.mdp 


define   = -DFLEXIBLE
constraints  = none
integrator   = steep
dt   = 0.002 ; ps !
nsteps   = 2000
nstlist  = 10
ns_type  = grid
rlist= 1.0
coulombtype  = PME
rcoulomb = 1.0
vdwtype  = cut-off
rvdw = 1.0
optimize_fft = yes
;
;Energy minimizing stuff
;
emtol= 10.0
emstep   = 0.01
---


thanks in advance 

  

1AKI.pdb
Description: application/aportisdoc
-- 
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] reasons for slow computation?

Hi all,

I am doing MD simulation on two almost identical protein-ligand systems with
GROMACS4.5.4 and amber99SB force fields.

Almost every single parameter I used for this two systems are the same (I
literally copied the mdp files for both), except that one has 65235 atoms
while the other has 65205 atoms, which is caused by the difference of 10
water molecules.

However, the 65235-atom one is significantly slower than the 65205-atom one,
the computational speed (performance) ratio is roughly 1:3.

I am really confused, since the only differences between them that I can
think of are:

1. The configuration of ligands, that is, alpha sugar vs beta sugar
2. number of water molecules, 19477 vs 19467
3. octahedral box size, ~726.119 nm^3 vs ~726.322 nm^3
4. probably the initial velocities, since I am used gen_seed= -1
5. the cpu specs, as I am using a cluster (I specified procs=72 for both
system and I assume they were assigned to different cpus randomly), which
consists of Intel Xeon E5450 quad-core processor, running at 3.0 GHz, and
Intel Xeon X5650 6-core processors running at 2.67 GHz

How come the performance could have a 1:3 difference?

Thanks for any suggestion!
Yun
-- 
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] Reduce the frequency to apply distance restrain

2011-10-10 Thread Li, Hualin

Dear GMX users,

   I am using pull code to make a distance restrain to my proteins and 
membrane,which looks like this:



 pull =   umbrella
 pull_geometry=   cylinder
 pull_vec1 =   0 0 1
 pull_r1  =   2.5
 pull_r0  =   2.5
 pull_dim =   N N Y ;# 3D

pull_start   =   yes ;# add COM distance to initial value (initial value = 
equilibrium value)
pull_ngroups =   32 ;# excluding the reference
pull_group0  =   membrane ;# the reference group - the membrane
pull_pbcatom0=   -1 ;# or -1 - important for PBC of groups larger than half 
box,
  ;# as here for membrane (see manual)
pull_group1  =   protein ;# the protein
pull_pbcatom1=   0 ;# here is no issue since protein is smaller than half 
the box
pull_rate1   =   0 ;# do not pull, just maintain distance!
pull_k1  =   800 ;# kJ mol^(-1) nm^(-2)

However, I have 32 protein to keep this local dynamic distance restrain (   
pull_geometry=   cylinder ), making the calculation goes very slowly. Is 
there any method to reduce the frequency to update the dynamic distance check 
and restrain please?

Thank you very much in advance.

Thanks,
Hualin 
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_rewritting_pdb




balaji nagarajan wrote:

Dear Users !

I have minimized the attached file using the gromacs43a1 and oplsaa 
force field using spc water molecules


I have used the following script for generating topology .
i minimized for 2000 steps , my doubt is when i rewrite the minimized 
pdb , in case of oplsaa
i was able to get all atoms , but in the case of the gromacs43a1 i am 
not getting the hydrogen atoms of the protein ,


how to solve this



http://www.gromacs.org/Documentation/Terminology/Force_Fields/United_Atom_Force_Field

-Justin


here is the steps which i have used

---
pdb2gmx -ignh -ff oplsaa -f 1AKI.pdb -o 1AKI_processed.gro -water spc
editconf -f 1AKI_processed.gro -o 1AKI_newbox.gro -c -d 0.9 -bt cubic
genbox -cp 1AKI_newbox.gro -cs spc216.gro -o 1AKI_solv.gro -p topol.top
grompp -f minim.mdp -c 1AKI_solv.gro -p topol.top -o em.tpr
mdrun -v -deffnm em
trjconv -f em.trr -o min.pdb -s em.tpr ( in this i gave the option 0 for 
the total system)

--
the minim.mdp


define   = -DFLEXIBLE
constraints  = none
integrator   = steep
dt   = 0.002 ; ps !
nsteps   = 2000
nstlist  = 10
ns_type  = grid
rlist= 1.0
coulombtype  = PME
rcoulomb = 1.0
vdwtype  = cut-off
rvdw = 1.0
optimize_fft = yes
;
;Energy minimizing stuff
;
emtol= 10.0
emstep   = 0.01
---


thanks in advance



--


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] reasons for slow computation?




Yun Shi wrote:

Hi all,

I am doing MD simulation on two almost identical protein-ligand systems 
with GROMACS4.5.4 and amber99SB force fields.


Almost every single parameter I used for this two systems are the same 
(I literally copied the mdp files for both), except that one has 65235 
atoms while the other has 65205 atoms, which is caused by the difference 
of 10 water molecules.


However, the 65235-atom one is significantly slower than the 65205-atom 
one, the computational speed (performance) ratio is roughly 1:3.


I am really confused, since the only differences between them that I can 
think of are:


1. The configuration of ligands, that is, alpha sugar vs beta sugar
2. number of water molecules, 19477 vs 19467
3. octahedral box size, ~726.119 nm^3 vs ~726.322 nm^3
4. probably the initial velocities, since I am used gen_seed= -1
5. the cpu specs, as I am using a cluster (I specified procs=72 for both 
system and I assume they were assigned to different cpus randomly), 
which consists of Intel Xeon E5450 quad-core processor, running at 3.0 
GHz, and Intel Xeon X5650 6-core processors running at 2.67 GHz




Point #5 is the one to check.  You *assume* they are running on different 
processors, but are they?  Are the nodes that are running the slow job fully 
functioning, or is one (or maybe more) down or overburdened with some other 
process(es)?  Try running the jobs independently so you can be sure there is no 
potential overlap.  There is no Gromacs-based reason for this to be happening. 
I strongly suspect the hardware is the problem.


-Justin


How come the performance could have a 1:3 difference?

Thanks for any suggestion!
Yun



--


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] Reduce the frequency to apply distance restrain




Li, Hualin wrote:

Dear GMX users,

   I am using pull code to make a distance restrain to my proteins and 
membrane,which looks like this:



 pull =   umbrella
 pull_geometry=   cylinder
 pull_vec1 =   0 0 1
 pull_r1  =   2.5
 pull_r0  =   2.5
 pull_dim =   N N Y ;# 3D

pull_start   =   yes ;# add COM distance to initial value (initial value = 
equilibrium value)
pull_ngroups =   32 ;# excluding the reference
pull_group0  =   membrane ;# the reference group - the membrane
pull_pbcatom0=   -1 ;# or -1 - important for PBC of groups larger than half 
box,
  ;# as here for membrane (see manual)
pull_group1  =   protein ;# the protein
pull_pbcatom1=   0 ;# here is no issue since protein is smaller than half 
the box
pull_rate1   =   0 ;# do not pull, just maintain distance!
pull_k1  =   800 ;# kJ mol^(-1) nm^(-2)

However, I have 32 protein to keep this local dynamic distance restrain (   
pull_geometry=   cylinder ), making the calculation goes very slowly. Is 
there any method to reduce the frequency to update the dynamic distance check 
and restrain please?



If you are maintaining 32 pull groups, your calculations will be horrendously 
slow, there's no real way around that without re-writing the code.  If you can 
do that and maintain accuracy, then the developers are likely to be interested 
in it.  Otherwise, accept the performance hit.


-Justin


Thank you very much in advance.

Thanks,
Hualin  
gmx-users mailing listgmx-users@gromacs.org

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

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



--


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


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

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

[gmx-users] FEP

2011-10-10 Thread Fabian Casteblanco

Hi all,

I have an additional question related to what Steven Neumann was
mentioning.  I actually have to do a molecule mutation.  I'm trying to
use Michael Shirts method  1) making small
changes 'alchemical' changes in the molecules and computing the free
energies by any method (BAR, TI, etc).  I'm specifically want to try
to use BAR at the end once I collect all the data.  This helped a lot
on clarification since it seemed that Justin's tutorial is essentially
a FEP except its using the BAR mathematical method for computing the
complete decoupling of the molecule rather than using the old FEP
mathematics of the exponential averaging formula.  So BAR is only
referring to the mathematical code used to calculate the overall free
energy for the FEP, correct?

My question is, for a mutation of a -CH3 group to a -H group, is it
better to simply run:
[+ from (Lambda=0 ,  R-CH3, full charges and interactions -STATE A)
-- (Lambda=1, R-CH, full charges and interactions -STATE B)]

OR

[1) from (Lambda=0 ,  R-CH3, STATE A : Charges and LJ Interactions: ON)
2)  (Lambda=?, -CH3 Charges: OFF ,LJ Interactions: ON and unmutated)
3)  (Lambda=?, R-CH3, -CH3 Charges: OFF ,LJ Interactions: OFF)
4)  (Lambda=?, R-CH3, -CH3 Charges: OFF ,LJ interactions: ON and Mutated to -H)
5)  (Lambda=1, R-CH3, -CH3  STATE B : Charges and LJ Interactions: ON)

Reason I'm asking is because when I try the first choice to do it
STATE A to STATE B in one step, when I reach Lambda=0.85 and above on
the NVT equilibration right after EM, I receive errors saying that
bonds are moving way to far off their constraints which leads me to
believe that the system is moving too far from where it was energy
minimized.  Errors such as:

Step 188, time 0.376 (ps)
LINCS WARNING
relative constraint deviation after LINCS:
rms 0.17, max 0.000636 (between atoms 9 and 68)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
  9 68   31.20.   0.1110  0.

Step 188, time 0.376 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.15, max 0.000531 (between atoms 9 and 68)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
  9 68   31.00.   0.1110  0.


**Please, if anybody can help, I would greatly appreciate it.  Thanks.
-- 
Best regards,

Fabian F. Casteblanco
Rutgers University --
Chemical Engineering
C: +908 917 0723
E:  fabian.castebla...@gmail.com
--
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: reasons for slow computation?

And another difference I noticed from .log files are:
..
Initial maximum inter charge-group distances:
two-body bonded interactions: 0.451 nm, LJ-14, atoms 3586 4808
  multi-body bonded interactions: 0.451 nm, Proper Dih., atoms 3586 4808
Minimum cell size due to bonded interactions: 0.496 nm

Optimizing the DD grid for 48 cells with a minimum initial size of 0.620 nm
The maximum allowed number of cells is: X 12 Y 12 Z 12
Domain decomposition grid 8 x 3 x 2, separate PME nodes 24
PME domain decomposition: 8 x 3 x 1
Interleaving PP and PME nodes
This is a particle-particle only node

Domain decomposition nodeid 0, coordinates 0 0 0

Using two step summing over 21 groups of on average 2.3 processes
...

for the slow one, while for the fast one:

Initial maximum inter charge-group distances:
two-body bonded interactions: 0.450 nm, LJ-14, atoms 2064 3014
  multi-body bonded interactions: 0.450 nm, Proper Dih., atoms 2064 3014
Minimum cell size due to bonded interactions: 0.494 nm


Optimizing the DD grid for 48 cells with a minimum initial size of 0.618 nm
The maximum allowed number of cells is: X 12 Y 12 Z 12
Domain decomposition grid 8 x 3 x 2, separate PME nodes 24
PME domain decomposition: 8 x 3 x 1
Interleaving PP and PME nodes
This is a particle-particle only node

Domain decomposition nodeid 0, coordinates 0 0 0

Using two step summing over 18 groups of on average 2.7 processes



Are these differences likely to generate huge performance difference?

Thanks,
Yun
-- 
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] FEP

2011-10-10 Thread Michael Shirts

 So BAR is only
 referring to the mathematical code used to calculate the overall free
 energy for the FEP, correct?

Yes.  The information required is the same, with the exception that
exponential averaging requires energy differences from only one state,
whereas BAR requires energy differences from both directions.  Since
you are likely running simulations at a range of states anyway,
there's no extra cost.

 My question is, for a mutation of a -CH3 group to a -H group, is it
 better to simply run:
 [+ from (Lambda=0 ,  R-CH3, full charges and interactions -STATE A)
 -- (Lambda=1, R-CH, full charges and interactions -STATE B)]

 OR

 [1) from (Lambda=0 ,  R-CH3, STATE A : Charges and LJ Interactions: ON)
 2)  (Lambda=?, -CH3 Charges: OFF ,LJ Interactions: ON and unmutated)
 3)  (Lambda=?, R-CH3, -CH3 Charges: OFF ,LJ Interactions: OFF)
 4)  (Lambda=?, R-CH3, -CH3 Charges: OFF ,LJ interactions: ON and Mutated to 
 -H)
 5)  (Lambda=1, R-CH3, -CH3  STATE B : Charges and LJ Interactions: ON)

Currently, you'd need to run three simulations to do this (will likely
be simplified somewhat in 4.6).

Set 1: turn R-CH3 charges off in a way that preserves the total charge.
Set 2: change CH3 LJ to H LJ
Set 3: Turn R-H charges on in a way that preserves the total charge.

Note that the first and last transformations will need only one two
states -- their energies will be VERY small.

 Reason I'm asking is because when I try the first choice to do it
 STATE A to STATE B in one step, when I reach Lambda=0.85 and above on
 the NVT equilibration right after EM, I receive errors saying that
 bonds are moving way to far off their constraints which leads me to
 believe that the system is moving too far from where it was energy
 minimized.  Errors such as:

 Step 188, time 0.376 (ps)
 LINCS WARNING
 relative constraint deviation after LINCS:
 rms 0.17, max 0.000636 (between atoms 9 and 68)
 bonds that rotated more than 30 degrees:
  atom 1 atom 2  angle  previous, current, constraint length
      9     68   31.2    0.   0.1110      0.

 Step 188, time 0.376 (ps)  LINCS WARNING
 relative constraint deviation after LINCS:
 rms 0.15, max 0.000531 (between atoms 9 and 68)
 bonds that rotated more than 30 degrees:
  atom 1 atom 2  angle  previous, current, constraint length
      9     68   31.0    0.   0.1110      0.

You probably have problems with the charge + LJ terms on the hydrogen.
 Note that you could possibly use soft core for the Coloumb
interactions for hydrogen -- it's sometimes causes sampling problems,
but for H's it probably doesn't matter.  I haven't done this approach
much so, so I can't tell for sure if it will work.
--
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] not guaranteed to be binary identical ?

Hi all,

I am doing my MD simulations piece by piece, with -maxh and -noappend
options, so that I can link pieces of trajectories together afterward.

But as I did part0001 with 48 cores, and part0002 with 72 cores, the log
file told me that:

  #nodes mismatch,
current program: 72
checkpoint file: 48

  #PME-nodes mismatch,
current program: -1
checkpoint file: 16

Gromacs binary or parallel settings not identical to previous run.
Continuation is exact, but is not guaranteed to be binary identical.

I do not quite understand what it really means by binary identical?

Would this affect my results? In other words, would using different # cores
for each part give me different conformational assembles from using the same
# cores each part?

Thanks for any help!
Yun
-- 
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] not guaranteed to be binary identical ?

Yun Shi wrote:

Hi all,

I am doing my MD simulations piece by piece, with -maxh and -noappend
options, so that I can link pieces of trajectories together afterward.

But as I did part0001 with 48 cores, and part0002 with 72 cores, the log
file told me that:

#nodes mismatch,
current program: 72
checkpoint file: 48

#PME-nodes mismatch,
current program: -1
checkpoint file: 16

Gromacs binary or parallel settings not identical to previous run.
Continuation is exact, but is not guaranteed to be binary identical.

I do not quite understand what it really means by binary identical?

Would this affect my results? In other words, would using different #
cores for each part give me different conformational assembles from
using the same # cores each part?

Several resources:

http://www.gromacs.org/Documentation/How-tos/Extending_Simulations#Exact_vs_binary_identical_continuation
http://www.gromacs.org/Documentation/Terminology/Reproducibility

-Justin

Thanks for any help!
Yun

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] Re: reasons for slow computation?




Yun Shi wrote:

And another difference I noticed from .log files are:
..
Initial maximum inter charge-group distances:
two-body bonded interactions: 0.451 nm, LJ-14, atoms 3586 4808
  multi-body bonded interactions: 0.451 nm, Proper Dih., atoms 3586 4808
Minimum cell size due to bonded interactions: 0.496 nm

Optimizing the DD grid for 48 cells with a minimum initial size of 0.620 nm
The maximum allowed number of cells is: X 12 Y 12 Z 12
Domain decomposition grid 8 x 3 x 2, separate PME nodes 24
PME domain decomposition: 8 x 3 x 1
Interleaving PP and PME nodes
This is a particle-particle only node

Domain decomposition nodeid 0, coordinates 0 0 0

Using two step summing over 21 groups of on average 2.3 processes
...

for the slow one, while for the fast one:

Initial maximum inter charge-group distances:
two-body bonded interactions: 0.450 nm, LJ-14, atoms 2064 3014
  multi-body bonded interactions: 0.450 nm, Proper Dih., atoms 2064 3014
Minimum cell size due to bonded interactions: 0.494 nm


Optimizing the DD grid for 48 cells with a minimum initial size of 0.618 nm
The maximum allowed number of cells is: X 12 Y 12 Z 12
Domain decomposition grid 8 x 3 x 2, separate PME nodes 24
PME domain decomposition: 8 x 3 x 1
Interleaving PP and PME nodes
This is a particle-particle only node

Domain decomposition nodeid 0, coordinates 0 0 0

Using two step summing over 18 groups of on average 2.7 processes



Are these differences likely to generate huge performance difference?



I would think these differences would not account for a threefold slowdown of 
one simulation relative to the other.  Please investigate the hardware issues I 
suggested before.


-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

[gmx-users] Re: FEP

2011-10-10 Thread Fabian Casteblanco

Thanks Michael for your help.  This really helps a lot.  Thank you!

On Mon, Oct 10, 2011 at 4:10 PM, Fabian Casteblanco
fabian.castebla...@gmail.com wrote:
 Hi all,

 I have an additional question related to what Steven Neumann was
 mentioning.  I actually have to do a molecule mutation.  I'm trying to
 use Michael Shirts method  1) making small
 changes 'alchemical' changes in the molecules and computing the free
 energies by any method (BAR, TI, etc).  I'm specifically want to try
 to use BAR at the end once I collect all the data.  This helped a lot
 on clarification since it seemed that Justin's tutorial is essentially
 a FEP except its using the BAR mathematical method for computing the
 complete decoupling of the molecule rather than using the old FEP
 mathematics of the exponential averaging formula.  So BAR is only
 referring to the mathematical code used to calculate the overall free
 energy for the FEP, correct?

 My question is, for a mutation of a -CH3 group to a -H group, is it
 better to simply run:
 [+ from (Lambda=0 ,  R-CH3, full charges and interactions -STATE A)
 -- (Lambda=1, R-CH, full charges and interactions -STATE B)]

 OR

 [1) from (Lambda=0 ,  R-CH3, STATE A : Charges and LJ Interactions: ON)
 2)  (Lambda=?, -CH3 Charges: OFF ,LJ Interactions: ON and unmutated)
 3)  (Lambda=?, R-CH3, -CH3 Charges: OFF ,LJ Interactions: OFF)
 4)  (Lambda=?, R-CH3, -CH3 Charges: OFF ,LJ interactions: ON and Mutated to 
 -H)
 5)  (Lambda=1, R-CH3, -CH3  STATE B : Charges and LJ Interactions: ON)

 Reason I'm asking is because when I try the first choice to do it
 STATE A to STATE B in one step, when I reach Lambda=0.85 and above on
 the NVT equilibration right after EM, I receive errors saying that
 bonds are moving way to far off their constraints which leads me to
 believe that the system is moving too far from where it was energy
 minimized.  Errors such as:

 Step 188, time 0.376 (ps)
 LINCS WARNING
 relative constraint deviation after LINCS:
 rms 0.17, max 0.000636 (between atoms 9 and 68)
 bonds that rotated more than 30 degrees:
  atom 1 atom 2  angle  previous, current, constraint length
      9     68   31.2    0.   0.1110      0.

 Step 188, time 0.376 (ps)  LINCS WARNING
 relative constraint deviation after LINCS:
 rms 0.15, max 0.000531 (between atoms 9 and 68)
 bonds that rotated more than 30 degrees:
  atom 1 atom 2  angle  previous, current, constraint length
      9     68   31.0    0.   0.1110      0.


 **Please, if anybody can help, I would greatly appreciate it.  Thanks.
 --
 Best regards,

 Fabian F. Casteblanco
 Rutgers University --
 Chemical Engineering
 C: +908 917 0723
 E:  fabian.castebla...@gmail.com




-- 
Best regards,

Fabian F. Casteblanco
Rutgers University --
Chemical Engineering PhD Student
C: +908 917 0723
E:  fabian.castebla...@gmail.com
--
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] CMAP for alanine dipeptide in Charmm27 ff

2011-10-10 Thread Jianguo Li

After checking the topology of my peptide, I found that every term in the cMAP 
section involve three consecutive residues. So I guess no cMAP term is required 
for di-ALA. 
 
Jianguo


--- On Mon, 10/10/11, César Ávila clav...@gmail.com wrote:


From: César Ávila clav...@gmail.com
Subject: Re: [gmx-users] CMAP for alanine dipeptide in Charmm27 ff
To: Jianguo Li ljg...@yahoo.com.sg, Discussion list for GROMACS users 
gmx-users@gromacs.org
Date: Monday, 10 October, 2011, 5:51 PM


v4.5.4 
As I commented above, I had to manually add an entrance for the cmap terms in 
the topology file as pdb2gmx would not generate them for the alanine dipeptide. 
There seems to be no problem for larger peptides. 
Cheers
Cesar


2011/10/10 Jianguo Li ljg...@yahoo.com.sg




which gromacs version are you using? cMAP is implemented in v4.5  or later

Jianguo






From: César Ávila clav...@gmail.com
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Sunday, 9 October 2011 12:07 AM
Subject: [gmx-users] CMAP for alanine dipeptide in Charmm27 ff



I would like to run REMD simulations on the alanine dipeptide using the 
Charmm27ff + CMAP. Still, after processing the pdb with pdb2gmx, I do not see 
any entrance referring to the cmap term in the topology file. Does this mean 
that Cmap won't be calculated? 


-- 
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


--
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

-- 
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] CMAP for alanine dipeptide in Charmm27 ff


On 11/10/2011 4:51 AM, César Ávila wrote:

v4.5.4
As I commented above, I had to manually add an entrance for the cmap 
terms in the topology file as pdb2gmx would not generate them for the 
alanine dipeptide. There seems to be no problem for larger peptides.

Cheers
Cesar



That sounds like a bug. Please describe your symptoms in a new issue 
here - http://redmine.gromacs.org http://redmine.gromacs.org/


Mark


2011/10/10 Jianguo Li ljg...@yahoo.com.sg mailto:ljg...@yahoo.com.sg

which gromacs version are you using? cMAP is implemented in v4.5 
or later

Jianguo


*From:* César Ávila clav...@gmail.com mailto:clav...@gmail.com
*To:* Discussion list for GROMACS users gmx-users@gromacs.org
mailto:gmx-users@gromacs.org
*Sent:* Sunday, 9 October 2011 12:07 AM
*Subject:* [gmx-users] CMAP for alanine dipeptide in Charmm27 ff

I would like to run REMD simulations on the alanine dipeptide
using the Charmm27ff + CMAP. Still, after processing the pdb with
pdb2gmx, I do not see any entrance referring to the cmap term in
the topology file. Does this mean that Cmap won't be calculated?


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

mailto: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
mailto:gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists


--
gmx-users mailing list gmx-users@gromacs.org
mailto: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
mailto: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] Re: reasons for slow computation?

Hi Justin,

I guess you are right, that some processors on that cluster appear to be
much slower than others.

But I am still wondering that, would the difference in initial maximum inter
charge-group distances (0.451 nm vs 0.450 nm) and minimum initial size of DD
gird (0.620nm vs 0.618nm) make the two simulations NOT comparable? Because I
want to compare the interactions of two different ligands with the same
protein.

Thanks,
Yun
-- 
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] Re: reasons for slow computation?


On 11/10/2011 1:40 PM, Yun Shi wrote:

Hi Justin,

I guess you are right, that some processors on that cluster appear to 
be much slower than others.


More likely is that the mapping of processes to processors is faulty, as 
Justin said.




But I am still wondering that, would the difference in initial maximum 
inter charge-group distances (0.451 nm vs 0.450 nm) and minimum 
initial size of DD gird (0.620nm vs 0.618nm) make the two simulations 
NOT comparable? Because I want to compare the interactions of two 
different ligands with the same protein.


That's just a detail of how the simulation is being implemented in 
parallel. There are a vast number of algorithmically equivalent ways to 
do this, and the initial conditions determine which is chosen. Since 
your initial conditions differ, so do the details.


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] Re: reasons for slow computation?