from:"Rama"

Thank you Justin ..
I will follow your Instructions ..
With Best Wishes,

R.David
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Re: [gmx-users] about trifloroehanol

Thank you justin..
I will try to adhere spacing
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[gmx-users] about trifloroehanol

 Hi all

 Very sorry for my stupid question .. I really work a lot on these problem

I wish to use Trifluroethanol  as solvent  for
my study ...

I Check the top file for G96 53a6 ff

It shows TFE with following lines ...


[ TFE ]
 [ atoms ]
   HT H 0.41000 0
   OT  OTFE-0.62500 0
 CH2T CHTFE 0.27300 0
   CT  CTFE 0.45200 0
  F1T  FTFE-0.17000 0
  F2T  FTFE-0.17000 0
  F3T  FTFE-0.17000 0
 [ bonds ]
   HTOTgb_1
   OT  CH2Tgb_18
 CH2TCTgb_27
   CT   F1Tgb_13
   CT   F2Tgb_13
   CT   F3Tgb_13
 [ angles ]
;  aiajak   gromos type
   HTOT  CH2T ga_50
   OT  CH2TCT ga_51
 CH2TCT   F1T ga_52
 CH2TCT   F2T ga_52
 CH2TCT   F3T ga_52
  F1TCT   F2T ga_49
  F1TCT   F3T ga_49
  F2TCT   F3T ga_49
 [ impropers ]
;  aiajakal   gromos type
 [ dihedrals ]
;  aiajakal   gromos type
   HTOT  CH2TCT gd_24


I draw  TFE with Avogadro software...

I get following pdb  ..

COMPNDUNNAMED
AUTHORGENERATED BY OPEN BABEL 2.3.0
HETATM1  C   LIG 1  -7.301   3.857   0.070  1.00
0.00   C
HETATM2  C   LIG 1  -6.798   2.416   0.102  1.00
0.00   C
HETATM3  F   LIG 1  -8.626   3.915   0.327  1.00
0.00   F
HETATM4  F   LIG 1  -7.094   4.399  -1.153  1.00
0.00   F
HETATM5  F   LIG 1  -6.668   4.631   0.977  1.00
0.00   F
HETATM6  O   LIG 1  -5.426   2.272  -0.294  1.00
0.00   O
HETATM7  H   LIG 1  -7.399   1.800  -0.574  1.00
0.00   H
HETATM8  H   LIG 1  -6.898   2.006   1.111  1.00
0.00   H
HETATM9  H   LIG 1  -5.299   2.795  -1.107  1.00
0.00   H
CONECT12345
CONECT1
CONECT21678
CONECT2
CONECT31
CONECT41
CONECT51
CONECT629
CONECT72
CONECT82
CONECT96
MASTER000000009090
END


I change pdb as follow to match the nomenclature with G96 53a6 ff
(Is it right or wrong )

OMPNDUNNAMED
AUTHORGENERATED BY OPEN BABEL 2.3.0
HETATM1   CT   TFE 1  -7.301   3.857   0.070  1.00
0.00   C
HETATM2 CH2T   TFE 1  -6.798   2.416   0.102  1.00
0.00   C
HETATM3  F1T   TFE 1  -8.626   3.915   0.327  1.00
0.00   F
HETATM4  F2T   TFE 1  -7.094   4.399  -1.153  1.00
0.00   F
HETATM5  F3T   TFE 1  -6.668   4.631   0.977  1.00
0.00   F
HETATM6   OT   TFE 1  -5.426   2.272  -0.294  1.00
0.00   O
HETATM7H   TFE 1  -7.399   1.800  -0.574  1.00
0.00   H
HETATM8H   TFE 1  -6.898   2.006   1.111  1.00
0.00   H
HETATM9   HT   TFE 1  -5.299   2.795  -1.107  1.00
0.00   H
CONECT12345

AFTER running pdb2gmx -ignh

 I got following error 

--
Program pdb2gmx, VERSION 4.5.4
Source code file: /build/buildd/gromacs-4.5.4/src/kernel/resall.c, line: 581

Fatal error:
Residue 'F' not found in residue topology database
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

I tried a lot ...
Please give me some suggestion ...
Thank you in Advance ...


Rama David ...
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Re: [gmx-users] about trifloroehanol

Hi to all


Sorry Justin , I try to correct spacing but now it stuck to another problem

pdb to TFE is as follow

OMPNDUNNAMED
AUTHORGENERATED BY OPEN BABEL 2.3.0
ATOM  1 CT   TFE 1  -5.510   2.534   0.093  1.00
0.00   C
ATOM  2 CH2T TFE 1  -6.061   1.111   0.155  1.00
0.00   C
ATOM  3 F1T  TFE 1  -5.017   2.899   1.300  1.00
0.00   F
ATOM  4  F2T TFE 1  -6.461   3.426  -0.251  1.00
0.00   F
ATOM  5  F3T TFE 1  -4.506   2.627  -0.806  1.00
0.00   F
ATOM  6   OT TFE 1  -7.065   0.921   1.164  1.00
0.00   O
ATOM  7H TFE 1  -5.248   0.409   0.367  1.00
0.00   H
ATOM  8H TFE 1  -6.500   0.837  -0.808  1.00
0.00   H
ATOM  9  HT  TFE 1  -6.742   1.339   1.982  1.00
0.00   H
CONECT12345
CONECT1
CONECT21678
CONECT2
CONECT31
CONECT41
CONECT51
CONECT629
CONECT72
CONECT82
CONECT96
MASTER000000009090
END


after giving pdb2gmx -ignh

It give following error
WARNING: atom HT is missing in residue TFE 1 in the pdb file
 You might need to add atom HT to the hydrogen database of building
block TFE
 in the file aminoacids.hdb (see the manual)


---
Program pdb2gmx, VERSION 4.5.4
Source code file: /build/buildd/gromacs-4.5.4/src/kernel/pdb2top.c, line:
1463

Fatal error:
There were 1 missing atoms in molecule Other, if you want to use this
incomplete topology anyhow, use the option -missing
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

---
 now I know go with missing is wrong ..But to check error I goes with
-missing flag .
the output confo.gro  is as follow

UNNAMED
6
1TFE OT1  -0.706   0.092   0.116
1TFE   CH2T2  -0.606   0.111   0.015
1TFE CT3  -0.551   0.253   0.009
1TFEF1T4  -0.502   0.290   0.130
1TFEF2T5  -0.646   0.343  -0.025
1TFEF3T6  -0.451   0.263  -0.081
   0.25590   0.25050   0.21060

The hydrogen attched to oxyge is missing ..
The entry to these hydrogen as HT is mentioned in pdb file ...

The warning message is self-explanatory.
I will be a very greatfull to you if you told me how to add HT
in aminoacids.hdb
Aminoacids.hdb file is as follow 

SER 2
11HN-CCA
12HGOGCBCA
*TFE 1
12HOCH2C*
THR 2
11HN-CCA
12HG1OG1CBCA
TRP 7
11HN-CCA
11HD1CD1CGNE1

So What line I have to add here???

Please suggest me the way out to get rid from error ..


Rama David
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Re: [gmx-users] about the frame selection

On Tue, May 15, 2012 at 11:59 AM, Anirban reach.anirban.gh...@gmail.comwrote:




 Thank you Anirban I proceed as you

mentioned...
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Re: [gmx-users] about the frame selection

Thank you ANIRBAN for your reply ..


 I think its better to remove the periodicity when you are going to start a
 fresh simulation with this protein.
   Could you told me how to remove the periodicity ???




 Thank you in advance ...





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[gmx-users] about the frame selection

Hi Gromacs Users ,
   I simulated a  4 peptide in a box .
 After completion of 30 ns simulattion , I extract
the particular time frame 29000 ps of my interest.
 Now I want these  frame for  my next simulations
study ..
In one simulation I want to keep the box size same as the
mentioned in extracted pdb  and in another one  I need to change the size
of box to
70 70 70


REMARKGENERATED BY TRJCONV
TITLE Protein in water t= 29000.0
REMARKTHIS IS A SIMULATION BOX
CRYST1   45.096   45.096   45.096  90.00  90.00  90.00 P 1   1
MODEL1

  So  my queries are like

1. Should I used the extracted frame directly for further study or
I need to remove the periodicity...??

 2 . to change the box size how to proceed ??
 Should I delete the line manually and adjust the box size


All suggestion are welcome ...


Than you in advance

rama david
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[gmx-users] TFE Proper Dihedral types...

Hi Gromacs Friends ..

I am using TFE (Trifluro Ethanol ) as a solvent for my simulation study..
I am using G96 53a6 ff

After the genbox -cp .. -cs tef.pdb -o mix.pdb

I count the no of solvent molecule , to update
topology ..

after Grompp I am facing following error
grompp -f minim.mdp -c mix.pdb -o em.tpr -p final.top


ERROR 1 [file topol-tef.itp, line 46]:
  No default Proper Dih. types

Excluding 3 bonded neighbours molecule type 'Protein'
Excluding 3 bonded neighbours molecule type 'SOL'

---
Program grompp, VERSION 4.5.4
Source code file: /build/buildd/gromacs-4.5.4/src/kernel/grompp.c, line:
1372

Fatal error:
There was 1 error in input file(s)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---


I checked the topology for TFE, Dihedral section is as follow ...


*
[ dihedrals ]
;  aiajakal functc0c1
c2c3c4c5
1 2 3 4 1gd_24
2 3 4 5 1*



 So what to resolve the problem ..
 All suggestions are welcome...

I will be a very greatfull to help 
Thank you in advance.
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Re: [gmx-users] TFE Proper Dihedral types...

On Tue, May 15, 2012 at 10:24 PM, Justin A. Lemkul jalem...@vt.edu wrote:




 The parameters are missing from ffbonded.itp, making the implementation
 incomplete.  You can obtain a TFE topology from ATB:

 http://compbio.biosci.uq.edu.**au/atb/download.py?molid=1655http://compbio.biosci.uq.edu.au/atb/download.py?molid=1655

 -Justin

 Thank you Justin ..
I obtain the topology from given link..

1. If you have some time , Could you tell me the way how to fix
   the missing parameter from ffbonded.itp ..???



With Best Wishes,
Rama David
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Re: [gmx-users] nvt equilibration output

2012-05-16 Thread rama david

Hi Priya,

My query is different than your problem ..


 I wondered Is you use position restrained in nvt...??
In position restrained protein comes togather or you remove
position restraind ...


Sorry for trouble you...

With Best wishes,

Rama David
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[gmx-users] (no subject)

2012-05-16 Thread rama david

Hi Gromacs Friends,

I plan  to simulate protein In Trifluoro Ethanol solvent
using G96 53a6 FF

Please help to define parameters in md.mdp

For water I am using following mdp file 

lincs_order= 4; also related to accuracy
; Neighborsearching
ns_type= grid; search neighboring grid cells
nstlist= 5; 10 fs
rlist= 0.9; short-range neighborlist cutoff (in nm)
rcoulomb= 0.9; short-range electrostatic cutoff (in nm)
vdw-type= Cut-off
rvdw= 1.4; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype= PME



For TFE and water mix of different conc , What should be  the mdp file
parameter  ???

I am using following ones..

Twin range cutt-off for nnonbonded interactions..
Short range cut-off 0.8 and long range 1.4 for both
coulombic and lennard-jones
Short range updates for every 5 step togather with pair
list..


Please give me valuable suggestion ..

Thank you in advance ..

With Best Wishes,
Rama David
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[gmx-users] Justin-lipid tutorials..

2012-05-19 Thread rama david

Hi Gromacs friends ..


I am doing justin Lipid-tutoria on lipid ..

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/01_pdb2gmx.html

I completed upto the ion addition and energy minimisation..
While doing equilibration I stuck with the following problem ..
1.  While NVT I found that protein are moving towards water and two layer
are getting separated
 2. Running  NPT on the lipid separated layers in nvt.gro  (get from above
nvt ) I found that both layer come to close again ...!!!
in NPT

So is it right or any wrong happen ??/

To solve the nvt lipid layer separation problem I am using the following
way mentioned by Justin advanced trouble shoot
page...

1.  Use position restrained upto 10 on lipid phosphate head group in z
direction..
 IN these case lipid layer still separated by small distance..
 2  I change the vanderwall radii to 0.350  and 0.320 (Tutorial mention to
0.375 )
to add more water  ..
  But in both time at nvt lipid layer get separated




Please give me valuable suggestion ..

Thank you in advance..

With Best wishes,
Rama David
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Re: [gmx-users] Justin-lipid tutorials..

2012-05-19 Thread rama david

Thank you Justin ..
..
I goes through these link ..
http://www.gromacs.org/Documentation/How-tos/Membrane_Simulations

Please Can any one clearly define me What is Lower Z and Upper Z in the
keepbyz.sh


Can keepbyz.sh use to remove the water in hydrophobic region without
affecting
the box dimension ...If yes Then what the value of Lower Z  and Upper Z


Thank you in Advance..

With Best Wishes,
Rama David..
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Re: [gmx-users] Justin-lipid tutorials..

2012-05-19 Thread rama david

Thank you Justin..
I am sorry Because I am going to ask you the stupid questions but very imp
to me ...

1.  Consider  your Tutorial In that Instead of using vanderwall radii
adjustment to add water ,
I  wish to use keepbyz.sh script ...

 In these case What would be the value of Lower and upper Z ..
 How to find out these hydropbhic region co-ordinate...

2.  From your reply , I Think Lower and upper  Z is the co-ordinate value ,
and in between these
Z-region no water molecule get added...



With Best Wishes,
Rama david
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[gmx-users] Justin umbrella sampling tutorial......

Hi Gromacs Friends,

   I am performing justin tutorial for umbrella sampling ..
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05_pull.html
I encounter with following problem while using the disatances.pl script

1. After command perl distances.pl  I got following message ...


   Use of uninitialized value $distance in concatenation (.) or string at
distances.pl line 30.
   readline() on closed filehandle IN at distances.pl line 16.
  What may be reason for these ..
2. What is the groups.txt ??
   Where it will find ?? Why it is needed??
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Re: [gmx-users] RE: Justin umbrella sampling tutorial...... (rama david)

On Wed, May 23, 2012 at 7:30 PM, Du Jiangfeng (BIOCH) 
j...@maastrichtuniversity.nl wrote:

 For your second problem: you have to create this file by writing the group
 numbers, which inform the script to decide which two groups

 Thank you... Du Jiangfeng


Yes problem get solve!!!

Thank you

With Best Wishes,
Rama David
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Re: [gmx-users] Justin umbrella sampling tutorial......

Thank you justin..
I solve script problem..

I have another query ..
As mention in tutorial , In step six , we have to do brief NPT
equilibration
npt_umbrella.mdp link is
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/Files/npt_umbrella.mdp
After these we have to run MD ...mdp file link is

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/Files/md_umbrella.mdp

1. In both case define is same..
In general When we are doing NPT we are position restrain whole
protein backbone ,
But in these case we are only restrain chain B...Please explain in
detail ...

2. The difference in mdp file is at gen_vel, and run time 100 ps for npt
, 10 ns for md
If both mdp file is same Then why to do separate npt and md

( Is the only reason is to generate velocity in npt simulation ???
Why we are not using velocity from
pull *(step five)* )

3 . If we are using the gen_vel = yes
continuation= yes

If continuation is yes, then why gen_vel is yes

Please shade some light on meaning of continuation and gen_vel

Thank you in advance

With Best Wishes,
Rama David
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Re: [gmx-users] Regarding error.

On Thu, May 24, 2012 at 10:20 AM, Seera Suryanarayana
paluso...@gmail.comwrote:

 Dear all gromacs users,
while running the command grompp -c
 1UZ9_em.gro -p 1UZ9.top -o 1UZ9_b4pr.tpr -f pr.mdp i am getting the
 following error.

   File input/output error:
   pr.mdp

   Please tell me how to over come this
 error


Hi Seera ,
 the error is self explainable,

 you dont  have pr.mdp in your working directory.
 Make pr.mdp as mention in tutorial

With Best Wishes,
Rama David




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Re: [gmx-users] Justin umbrella sampling tutorial......

Hi Justin,

Thank you for your Reply

Before start tutorial I read your paper, It help me
a lot to understand the concept of umbrella sampling...

But truly I not understand the part in six step
 why to use define -DPOSRES_B  and not -DPOSRES,
I think I miss it ...


I will be a very greatfull to you, if you shade
some light on these 

Sorry for trouble

Thank you in advance

With best wishes,
Rama David



Thank you in advance

With Best Wishes,

Rama David
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Re: [gmx-users] Justin umbrella sampling tutorial......

Thank you for your reply,

I am asking you again same question, EXTREMELY SORRY for my stupidity,

In step six , I unable to differentiate npt and production run by
mdp file as usualy we find difference by define term,

I think I get meaning upto reason why to use -DPOSRES_B,
but I want to know if we are using same mdp file in both condition
means the npt equilibriation is as same as md production ,

Then why to do npt, just run production md  with  DPOSRES_B


With my  best Wishes ,
Rama David
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Re: [gmx-users] Justin umbrella sampling tutorial......

Thank you Justin for these correct explanation
Its really clear my lot of queries..


 For the tutorial, NPT is conducted with restraints on all protein heavy
 atoms.  The production runs are conducted by restraining only one chain for
 practical reasons.



 These is my question ;

If we are doing NPT with restraints on all protein atom and production run
by conducted by restraining only one chain for protein...

means NPT and productin run mdp files should be different , Where these
information in mdp files???
It my request to you please tell me why these mdp files are almost same in
parameter ..

(Where you mentioned in mdp for npt to do restraints on all proteins heavy
atoms and for production md restraining only
one chain ..)



Please accept my apology if I unable to explain you my problem



Thank you in advance ...

With best wishes,
Rama david
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Re: [gmx-users] trjconv_snapshot

On Thu, May 24, 2012 at 5:24 PM, Turgay Cakmak turgaycakma...@gmail.comwrote:


 Hi Gromacs users,

 I have a problem getting a snapshots using trjconv. If you could help me,
 I would be very grateful. Below, I try to explain what I did and problem
 happened.
 Firstly, I have done 10ns long simulation (several peptides in a box). And
 then, using the outputs of that simulation (conf10ns.gro and 10ns.cpt
 files), I extend the simulation 10 ns more and I get conf20ns.gro,
 trj20ns.xtc,….

 Then I used the following to get snapshot of the last frame.

 trjconv –f traj20ns.xtc –s topol.tpr –b 1 –e 1 –o
 snapshot20ns.gro  (Note: traj20ns.xtc is not a full trajectory, it
 just a trajectory of second 10ns simulation)

 When I looked these two files (conf20ns.gro and snapshot20ns.gro) at the
 VMD, they were completely different configurations. As far as I know, the
 last frame is written in conf20ns.gro. So they must be the same. What is
 wrong here?

 By the way, I defined dt=0,002, nstxout=1000 and nsteps=500 in my mdp
 file.
 Thanks in advance,

 Turgay


Catenate two trajectory with help of trjcat -h

to get snapshot of particular time use trjconv -dump time
use appropriate pbc option


you are using -b 1 -e 1

means the snapshot at 10 ns
So I think conf20.gro is snapshot at 20 ns  so they may differ ...


With Best Wishes,
Rama David
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Re: [gmx-users] trjconv_snapshot

Hi ,

You run extended simulation of 10 ns  on your first  10ns simulation .
You get traj20ns.xtc.
these new trajectory contain all the tme frame from onwards 10ns.
So if you are giving command

trjconv –f traj20ns.xtc –s topol.tpr –b 1 –e 1 –o
snapshot20ns.gro  (Note: traj20ns.xtc is not a full trajectory, it just
a trajectory of second 10ns simulation)

with traj20ns.xtc if you need 20 ns snapshot use -b 2 -e 2


With Best Wishes,

Rama David
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Re: [gmx-users] Re: Justin umbrella sampling tutorial......

Thank you Thomas and Justin for your valuable suggestion.
Thomas and Justin, my Query is as follow..

In step six ..We are doing NPT equilibration followed by production run
The mdp files for both is same(Except the time of run and saving of
output)
So why the two mdp are same?  Why we not restrain total protein for NPT
equilibration (-DPOSRES)
and then only POSRES_B (Position restrain on B chain, remove position
restrain from other chain)
for production run..(these we follow generally)???

The main reason of confusion to me is the same mdp file in
Equilibration(npt_umbrella.mdp )
and production run (md_umbrella.mdp). So what is the difference between the
NPT equilibration
and production run.???

As per Thomas explanation I interpret the following Answer to my Queries..
Please tell me  these are right or wrong 


*So if you want to calculate some equilibrium property of a protein in
water you do
 first a preperation simulation to equilibrate the system (NVE, NVT or NPT
- depending
for what ensemble you want the property).Normally during this you put
position restraints
to the protein backbone, so that the protein structure does not gets
disturbed during the part where you equilibrate the water. but if your
protein is fairly stable / rigid, you don't need these restraints.*

So as the protein is stable thats why we are not using the position
restrained in NPT..
That is the reason the npt_umbrella.mdp and md_umbrella.mdp looks same.



Please accept my apology if I interpret any wrong and if unable to explain
you my query..

Thanks to Justin and Thomas for there valuable guidance

I will be a very greatfull to you if you help me to solve my simple  query..


Thank you in advance...


With Best Wishes,
Rama David.
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Re: [gmx-users] Re: Justin umbrella sampling tutorial......

 Thank you Thomas and Justin for your valuable suggestion.
 Thomas and Justin, my Query is as follow..

 In step six ..We are doing NPT equilibration followed by production run
 The mdp files for both is same(Except the time of run and saving of
 output)
 So why the two mdp are same?  Why we not restrain total protein for
 NPT equilibration (-DPOSRES)
 and then only POSRES_B (Position restrain on B chain, remove position
 restrain from other chain)
 for production run..(these we follow generally)???

 The main reason of confusion to me is the same mdp file in
 Equilibration(npt_umbrella.mdp )
 and production run (md_umbrella.mdp). So what is the difference between
 the NPT equilibration
 and production run.???

 As per Thomas explanation I interpret the following Answer to my Queries..
 Please tell me  these are right or wrong 


 *
 So if you want to calculate some equilibrium property of a protein in
 water you do
  first a preperation simulation to equilibrate the system (NVE, NVT or NPT
 - depending
 for what ensemble you want the property).Normally during this you put
 position restraints
 to the protein backbone, so that the protein structure does not gets
 disturbed during the part where you equilibrate the water. but if your
 protein is fairly stable / rigid, you don't need these
 restraints.(Thomas Explanation)
 *
 my Interpretation is as follow 



 So as the protein is stable thats why we are not using the position
 restrained in NPT..
 That is the reason the npt_umbrella.mdp and md_umbrella.mdp looks same.



 Please accept my apology if I interpret any wrong and if unable to explain
 you my query..

 Thanks to Justin and Thomas for there valuable guidance

 I will be a very greatfull to you if you help me to solve my simple
 query..


 Thank you in advance...


 With Best Wishes,
 Rama David.





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Re: [gmx-users] Re: Justin umbrella sampling tutorial......

Thank you Justin for reply...


 More or less.  The special case with what you're doing in the tutorial is
 that you have no initiating velocities in each window; you only have
 coordinates. That's why it makes sense to do a bit of equilibration in each
 window first, generating velocities and re-equilibrating the system.

 -Justin


  In npt_umbrella.mdp we have

 gen_vel = yes

 The command line in tutorial is

grompp -f npt_umbrella.mdp -c conf0.gro -p topol.top -n index.ndx -o npt0.tpr
...
grompp -f npt_umbrella.mdp -c conf450.gro -p topol.top -n index.ndx -o npt22.tpr


So if I modify the process as follow, Then is the need of equilibration
(Can we skip equilibration and run production md)

 use -t flag with cpt ( to give velocity of the previous run ) file
continuation = yes
 gen_vel = no .

Is these alternative process is right or totally wrong..???

Please give me a valuable suggestion.

Thank you in advance.

With Best Wishes,
Rama David.
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Re: [gmx-users] Re: Justin umbrella sampling tutorial......

Thank you Justin..



 Is these alternative process is right or totally wrong..???


 Using the checkpoint in this instance is wrong.  The only checkpoint you
 have accessible to you at that point is from the end of the pulling
 simulation and corresponds to the final state of the system.  Applying
 these velocities to the intermediate configurations along the reaction
 coordinate is likely to do weird and unreliable things to the trajectory.
  It is more robust to run NPT and then data collection, or as I said
 before, proceed immediately to a continuous data collection (with gen_vel =
 yes!) and discard the initial few ns of data as equilibration.  In theory,
 this procedure is no different than any other simulation that one conducts.


 Check point file has velocity of the last co-ordinates and we are using
middle configuration..
Thank you for explaination ...

I have another query..

In npt equilibration can I use define = -DPOSRES (Position restrain all the
protein along the chain B)
 and in production md define = -DPOSRES_B ( Position restrain for chain B
only..)  ???


If not What is appropriate reason???

Thank you in advance...

With Best Wishes,
Rama David.
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Re: [gmx-users] Re: Justin umbrella sampling tutorial......

Thank you Justin for giving your valuable time to solve
my stupid problems.




 You can use either.  I have never tried it, but there is no reason to
 believe there will be any substantive reason during data collection.  The
 production MD period is significantly longer than the equilibration, and
 the results will likely turn out the same, when considering error
 estimates.  Sufficient sampling of any series of simulations should
 converge.


 -Justin



With Best Wishes,
Rama David.
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[gmx-users] umbrella windows...

2012-06-01 Thread rama david

Hi Gromacs Friends,

I am doing Justin-Umbrella sampling tutorial...
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/06_umbrella.html

After pulling I found the Chain A is moving away from protofibril but
reaches up to the other end of the cell..
So Is these situation Satisfy the Minimum image condition??? or Am I doing
some wrong ..???

as tutorial Says..
GROMACS calculates distances while simultaneously taking periodicity into
account. This, if you have a 10-nm box, and you pull over a distance
greater than 5.0 nm, the periodic distance becomes the reference distance
for the pulling, and this distance is actually less than 5.0 nm! This fact
will significantly affect results, since the distance you *think* you are
pulling is not what is *actually* calculated.

My Query is on very basic concept...
tutorial says

In this example, we will be sampling COM distances from 0.5 - 5.0 nm along
the z-axis using roughly 0.2-nm spacing. The following example commands may
or may not be literally correct (the frame numbers may differ), but will
serve as an example as to how to run grompp on separate coordinate files to
generate all 23 inputs (note as well that 23 is the amount of windows
required to obtain 0.2-nm spacing over roughly 4.5 nm;
my summary_distances.dat has following lines..

00.5011713
10.5068762
20.4948514
..
.
.
1600.6993698
so my 1st configuration will be at 0 (0.5011713) and 160 (0.69936) .Is it
right???

I choose total 28 windows instead of 23 ...So is it good or bad ???

Thank you in Advance...
With Best Wishes,
Rama David
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[gmx-users] About extend the run,,

2012-06-02 Thread rama david

Hi Gromacs Friends,

I run a Production run with saving the  co-ordinates and velocity
after every 500 steps for 20ns..
Now I want to extend the run but with saving the  co-ordinates and velocity
after every 1000 steps for next 30ns (total 50ns)

To perform these task I am using following command
1. grompp -f New mdp file just change in  saving output  -t .cpt  -c
.gro file(gro file from position restrained run )  -o new.tpr


2. tpbconv -s new.tpr -0 extend.tpr  -extend 3

3. mdrun -v -deffnm extend  -cpi .cpt -append

Is these approach is correct??

Second query;

To rerun the crash run, users give .cpt file as input to -mdrun,
My query is, There are two cpt file a) pre.cpt  b) .cpt ,
So which one has to given as input???

All suggestion are welcome...

With Best Wishes,
Rama david
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Re: [gmx-users] About extend the run,,

2012-06-02 Thread rama david

Thank you Justin for quick reply 

On Sat, Jun 2, 2012 at 8:12 PM, Justin A. Lemkul jalem...@vt.edu wrote:



 To perform these task I am using following command
 1. grompp -f New mdp file just change in  saving output  -t .cpt  -c
 .gro
 file(gro file from position restrained run )  -o new.tpr


 2. tpbconv -s new.tpr -0 extend.tpr  -extend 3

 3. mdrun -v -deffnm extend  -cpi .cpt -append

 Is these approach is correct??


 No.  The new.tpr file contains instructions to run from 20 - 30 ns.
  There is no need to then invoke tpbconv.  You would also need a new
 invocation of mdrun, since the output frequencies won't match.  You don't
 want to append those files with mdrun (nor will the checkpoint file likely
 let you)


Extremely Sorry for my carelessness , New mdp files means the same as
previous, with same number of steps, but just change in output frequency

So as per your recommendation and experience  Is any alternative to do
these from 20 ns???



 Second query;

 To rerun the crash run, users give .cpt file as input to -mdrun,
 My query is, There are two cpt file a) pre.cpt  b) .cpt ,
 So which one has to given as input???


 Use gmxcheck to understand the contents of each.  The timestamp will also
 tell you a difference, as will reading mdrun -h for an explanation of what
 the -cpt option is doing


As per the link..
http://www.gromacs.org/Documentation/File_Formats/Checkpoint_File
I interpreted following things..

1. I have to use the state.cpt , but in the case  problem to these I have
to use prev.cpt,  I can check there
content by gmxcheck..

 But my Query is What are may be the potential problems ?? and how to
find them ??

Crash the run is very often with my system, that why I am worried..
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Re: [gmx-users] About extend the run,,

2012-06-02 Thread rama david

 Thank You  for Quick reply Justin...

On Sat, Jun 2, 2012 at 8:58 PM, Justin A. Lemkul jalem...@vt.edu wrote:


 You'll get a mismatch in your files (checkpoint, trajectory, energy) in
 terms of frame interval.  You should not try to append to these files or
 extend the run.  Just run a new simulation from 20 - 30 ns.  The grompp
 command was correct, assuming you set tinit = 2 in the .mdp file and
 setting nsteps appropriately to give another 10 ns.  Then run it as a new
 simulation.  It will still be an extension of the first simulation (since
 the .cpt preserves the previous state), but without the mdrun -cpi -append
 mechanism, which in this case you don't want (or possibly can't use)


I will follow your advice..





 Second query;

To rerun the crash run, users give .cpt file as input to -mdrun,
My query is, There are two cpt file a) pre.cpt  b) .cpt ,
So which one has to given as input???


Use gmxcheck to understand the contents of each.  The timestamp will
 also
tell you a difference, as will reading mdrun -h for an explanation of
 what
the -cpt option is doing


 As per the link..http://www.gromacs.org/**Documentation/File_Formats/**
 Checkpoint_Filehttp://www.gromacs.org/Documentation/File_Formats/Checkpoint_File
 I interpreted following things..

 1. I have to use the state.cpt , but in the case  problem to these I have
 to use
 prev.cpt,  I can check there
 content by gmxcheck..

  But my Query is What are may be the potential problems ?? and how to
 find
 them ??

 Crash the run is very often with my system, that why I am worried..


 If you're getting frequent crashes, you should investigate why this is
 happening rather than just plowing ahead.  Are there error messages in the
 .log or stdout/stderr output?  Are your energetic terms sensible?  If the
 system is crashing due to physical instability, you're wasting your time
 producing junk. If the crashes are occurring due to hardware or filesystem
 instability, that's something to take up with your sysadmin.


 -Justin

Thank you For Advice...
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[gmx-users] LINCS warnings

Hi Gromacs Friends ..

I am trying to simulate octa-peptide in water model spc using G96 53a6
force field.
my aim is to study the self assembly nature of these octapetide.
I did following type of arrangment.

I make antiparrallel arrangment of four peptide with distance of 0.5 nm in
y direction,
Then I translate these layer  in z direction, Such that separation in each
layer is 0.5 ,

I arranged six layer in Z direction(total 24 peptide 6 * 4=24 ),

I did Steepest Descent

Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax  100

Double precision normally gives you higher accuracy.

writing lowest energy coordinates.

Steepest Descents converged to machine precision in 108 steps,
but did not reach the requested Fmax  100.
Potential Energy  = -9.2318734e+04
Maximum force =  6.8985820e+04 on atom 1359
Norm of force =  9.8921991e+02


For nvt run I got Lincs Error


Step 772, time 1.544 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.001014, max 0.009497 (between atoms 1360 and 1358)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   1359   1358   61.40.1000   0.1004  0.1000

Step 773, time 1.546 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.003091, max 0.027499 (between atoms 1359 and 1358)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   1360   1358   32.10.0991   0.0985  0.1000
   1359   1358   90.00.1004   0.1027  0.1000

---
Program mdrun, VERSION 4.5.4
Source code file: /build/buildd/gromacs-4.5.4/src/mdlib/constr.c, line: 176

Fatal error:
Too many LINCS warnings (1001)
If you know what you are doing you can adjust the lincs warning threshold
in your mdp file
or set the environment variable GMX_MAXCONSTRWARN to -1,
but normally it is better to fix the problem
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

Carry Me Away (Motors)


When I check the website at http://www.gromacs.org/Documentation/Errors

I come to know that system is unstable or not properly energy minimised
(e+04) is the source for such type of errors.

But Truly I dont Want to change the arrangment (distance 0.5 nm),

Please Help me to solve the above problem,

All suggestion are welcome



With Best Wishes,
Rama David
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Re: [gmx-users] LINCS warnings

Hi MARK,
 Thank you to your  Quick reply,
Please accept my apology for incomplete information...

 I did simulationm of single, Double and four peptide..

I also tried following
I make antiparrallel arrangment of four peptide with distance of 0.4 nm in
y direction,
Then I translate these layer  in z direction, Such that separation in each
layer is 0.4 ,

I arranged eight layer in Z direction(total 24 peptide 8 * 4=32 ),
All things was right.



Thank you in Advance

With Best Wishes,
Rama David
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Re: [gmx-users] LINCS warnings

Hi Mark,

I did simulation of the same system in vacuum, and system behave the
normally,
So the instability  in the system is due to the spc Water model???
As per the link http://www.gromacs.org/Documentation/Terminology/Blowing_Up

I think the source is (Please tell me is it right..?? or any else reason  )
last option :
you have a single water molecule somewhere within the system that is
isolated from the other water molecules.


How to find such water molecule and solve the problem??


Thank you in Advance .

With Best Wishes,
Rama David
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Re: [gmx-users] LINCS warnings

Hi  Justin, thank you for quick reply.
You are right I have practicle result, And I want to replicate them..

Thank you for your suggestion..

With Best Wishes,
Rama David

On Mon, Jun 11, 2012 at 3:58 PM, Justin A. Lemkul jalem...@vt.edu wrote:



 On 6/11/12 6:23 AM, rama david wrote:


 Hi Mark,

 I did simulation of the same system in vacuum, and system behave the
 normally,
 So the instability  in the system is due to the spc Water model???
 As per the link http://www.gromacs.org/**Documentation/Terminology/**
 Blowing_Up http://www.gromacs.org/Documentation/Terminology/Blowing_Up


 The water model is not the problem.  Your solvated system has clashes that
 cause instability.  In vacuo, your solute has greater freedom to shift
 around.


  I think the source is (Please tell me is it right..?? or any else reason
  )
 last option :
 you have a single water molecule somewhere within the system that is
 isolated
 from the other water molecules.


 How to find such water molecule and solve the problem??


 I think this is unlikely.  If you have any isolated waters, they might be
 sandwiched somewhere in your protein layers and should be easy to spot.
  The best strategy is to use the output of EM to your advantage.  Look at
 the atom that had the highest force on it.  What is it near?  What might it
 be clashing with?  What if you run EM in vacuo, followed by solvation, and
 another round of EM?

 From your earlier description, it seems to me that the system has been
 constructed to replicate some known experimental spacing, but doing so does
 not guarantee that whatever peptide structure you are replicating will
 necessarily produce a sensible result, or one that is free from clashes.
  Hence, you need to refine the model before continuing.

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[gmx-users] simulated annealing mdp

Hi Gromacs Friends,

I planed to do simulated annealing...
My protocol is as follow
( forcefield G96 53a6   spc water model)

1. nvt at 310 k for 100 ps
2. Sa (mdp is posted below )
3. NPT at 310 k for 100 ps

Is it right ??

Please suggest me improvements...

Sa mdp file

title= gromacs
define= -DPOSRES; position restrain the protein

nstcomm= 1
comm-mode= Linear; Run parameters
integrator= md; leap-frog integrator
nsteps= 50; 2 * 5 = 100 ps
dt= 0.002; 2 fs
; Output control
nstxout= 1000; save coordinates every 0.2 ps
nstvout= 1000; save velocities every 0.2 ps
nstenergy= 1000; save energies every 0.2 ps
nstlog= 1000; update log file every 0.2 ps
; Bond parameters
continuation= yes; Restarting after NVT
constraint_algorithm = lincs; holonomic constraints
constraints= all-bonds; all bonds (even heavy atom-H bonds)
constrained
lincs_iter= 1; accuracy of LINCS
lincs_order= 4; also related to accuracy
; Neighborsearching
ns_type= grid; search neighboring grid cells
nstlist= 5; 10 fs
rlist= 0.9; short-range neighborlist cutoff (in nm)
rcoulomb= 0.9; short-range electrostatic cutoff (in nm)
vdw-type= Cut-off
rvdw= 1.4; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype= PME; Particle Mesh Ewald for long-range
electrostatics
pme_order= 4; cubic interpolation
fourierspacing= 0.16; grid spacing for FFT
; Temperature coupling is on
tcoupl= V-rescale; modified Berendsen thermostat
tc-grps= Protein Non-Protein; two coupling groups - more
accurate
tau_t= 0.10.1; time constant, in ps
ref_t= 310 310; reference temperature, one for each group,
in K
; Pressure coupling is on
pcoupl= Parrinello-Rahman; Pressure coupling on in NPT
pcoupltype= isotropic; uniform scaling of box vectors
tau_p= 2.0; time constant, in ps
ref_p= 1.0; reference pressure, in bar
compressibility = 4.5e-5; isothermal compressibility of water, bar^-1
; Periodic boundary conditions
pbc= xyz; 3-D PBC
; Dispersion correction
DispCorr= EnerPres; account for cut-off vdW scheme
; Velocity generation
gen_vel= no; Velocity generation is off
; Simulated annealing
annealing   = single single
annealing_npoints=  4  4
annealing_time  =  0  200  400 600 0 200 400 600
annealing_temp  = 310 323 300 310  310 323 300 310




Thank you in advance

With Best Wishes,
Rama David
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[gmx-users] Press Equilibration

Hi Gromacs Friends,

I did NPT for 100 ps with folowing parameter

; Temperature coupling is on
tcoupl= V-rescale; modified Berendsen thermostat
tc-grps= Protein Non-Protein; two coupling groups - more
accurate
tau_t= 0.10.1; time constant, in ps
ref_t= 310 310; reference temperature, one for each group,
in K
; Pressure coupling is on
pcoupl= Parrinello-Rahman; Pressure coupling on in NPT
pcoupltype= isotropic; uniform scaling of box vectors
tau_p= 2.0; time constant, in ps
ref_p= 1.0; reference pressure, in bar


I got foolowing result by using g_energy

Energy  Average   Err.Est.   RMSD  Tot-Drift
---
Pressure   -3.99675   0.66518.604   -2.89716  (bar)


Is it is right??
Is the system is equilibrated or I need to give more time ?
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Re: [gmx-users] simulated annealing mdp

THANK YOU Justin,
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[gmx-users] Re: Press Equilibration

On Tue, Jun 12, 2012 at 4:40 PM, rama david ramadavidgr...@gmail.comwrote:


 Hi Gromacs Friends,

 I did NPT for 100 ps with folowing parameter

 ; Temperature coupling is on
 tcoupl= V-rescale; modified Berendsen thermostat
 tc-grps= Protein Non-Protein; two coupling groups - more
 accurate
 tau_t= 0.10.1; time constant, in ps
 ref_t= 310 310; reference temperature, one for each group,
 in K
 ; Pressure coupling is on
 pcoupl= Parrinello-Rahman; Pressure coupling on in NPT
 pcoupltype= isotropic; uniform scaling of box vectors
 tau_p= 2.0; time constant, in ps
 ref_p= 1.0; reference pressure, in bar


 I got foolowing result by using g_energy

 Energy  Average   Err.Est.   RMSD  Tot-Drift

 ---
 Pressure   -3.99675   0.66518.604   -2.89716  (bar)


 Is it is right??
 Is the system is equilibrated or I need to give more time ?

 I am worried because of avg is -ve ...
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Re: [gmx-users] Press Equilibration

thank you for Quick reply
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Re: [gmx-users] simulated annealing mdp

Hello Justin and Ravi,

Lets explain me Why I  did simulated anealing?? ..


I synthesise peptide and I have experimental data for its self assembly,
I just want to reproduced these data.


I arranged the 32 protein in axis to petide fibre, in antiparrallel Beta
sheet structure.
I dont have crystal structure ,

Thats why I did SA in the hope that after these the side chain may be get
properly oriented with respect to each other.That will give me good
structure for production run.
 I also run system withought SA , but I get good result by following SA
protocol.

In posrestrain only backbone is restrained and the sidechain is free to
move, So I
think it may be help to achieve my goal.

After these I also plan  to use SA as production run, then compare the
result with previous protocols.

Please give valuable suggestion to improve my study protocol..


With Best Wishes,
Rama David.
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Re: [gmx-users] simulated annealing mdp

Thank you for reply
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[gmx-users] Lipid-protein simulation....

2012-06-26 Thread rama david

Hi Gromacs Friends,

 I completed Justin-Lipid Tutorial.
I plan to simulate protein-lipid system  to study protein-lipid interaction.
My Query is like

1. I plan to use DPPC (128) lipid from Tieleman Website.
  I removed its periodicity as per tutorial instruction..
  I found that I need the z box Dimension more than 6.59650.
  ( I not Change x-y box Dimension , As it affect the equilibrated DPPC layer).
So with help of editconf command I changed the Z box Dimension to 8.00
while  x and y are same .

Is these process is right or any good suggestion in my work-flow ???

2. I wish to put lipid membrane away from protein ( Protein is not
embedded in lipid ).
Should I use InflateGro?? Should I use Strong position restrain
during Energy minimisation???


please give me valuable Guidance

With Best Wishes and regards
Rama
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[gmx-users] Re: Lipid-protein simulation....

2012-06-26 Thread rama david

On Tue, Jun 26, 2012 at 9:32 PM, rama david ramadavidgr...@gmail.com wrote:
 Hi Gromacs Friends,

  I completed Justin-Lipid Tutorial.
 I plan to simulate protein-lipid system  to study protein-lipid interaction.
 My Query is like

 1. I plan to use DPPC (128) lipid from Tieleman Website.
  I removed its periodicity as per tutorial instruction..
  I found that I need the z box Dimension more than 6.59650.
  ( I not Change x-y box Dimension , As it affect the equilibrated DPPC layer
 I deleted SOL molecule from DPPC layer, I plan to solvate  system
after catenation
of lipid and protein gro file).
 So with help of editconf command I changed the Z box Dimension to 8.00
 while  x and y are same .

 Is these process is right or any good suggestion in my work-flow ???

 2. I wish to put lipid membrane away from protein ( Protein is not
 embedded in lipid ).
    Should I use InflateGro?? Should I use Strong position restrain
 during Energy minimisation???


 please give me valuable Guidance

 With Best Wishes and regards
 Rama
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[gmx-users] Fwd: About Justin Lipid-protein simulation tutorial

2012-06-26 Thread rama david

Hi Gromacs Friends,
    I am doing Justin-lipid tutorialer
http://bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html

In these the npt.mdp has a parameter
refcoord_scaling = com
Why these parameter is introduced in NPT of lipid-protein simulation
 and not use in Lysozyme in water simulation ???

Please give the detail on why to use these parameter??


Thank you in advance

With best Wishes and Regards,
Rama
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Fwd: [gmx-users] Fwd: About Justin Lipid-protein simulation tutorial

2012-06-27 Thread rama david

 Thank you Justin for your Explaination

 Please Would you me the Reason Why these parameter is present in
 Equilibration mdp and
 not in production run mdp file ( for both lysozyme and lipid simulation )

 With Best Wishes and regardsRama
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Re: [gmx-users] Fwd: About Justin Lipid-protein simulation tutorial

2012-06-27 Thread rama david

Thank you Justin,

But you not added these parameter to the
Umbrella sampling NPT file.
Is any reason not to use these parameter  in Umbrella sampling??

I run the simulation of peptide withought any
refcoord_scaling = com in mdp  file
and now  is it will affect result  significantly??
Is it wrong simulation???

How to check these parameter affect my result sensitivity???

Please give me valuable guidance to solve my query..

With Best Wishes and regards,
Rama David
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[gmx-users] Fwd: Determine sec structure by MD

2012-06-28 Thread rama david

Hi Gromacs Friends,

        I have the experimental result of change in Secondary
structure of peptide from random coil to Beta sheet, as  the conc
increases
( but  not know the Parallel or anti-parallel )

                       I run Simulation of ( 30ns ) two peptide in random coil
structure put sufficiently apart  (2.4 nm) so they are not interacting to each
other initially, I found they are coming close to each other in anti-parallel
fashion, But they remain in random coil.To extend these study I run simulation
of four peptide they also come close to each other in anti-parallel way
(Show the change in secondary structure from random coil to
anti-parallel beta sheet)
After these I put the peptide in anti-parallel way  to form the fiber structure,
they show the some parallel and anti-parallel  arrangement in fiber.

Note- If I put the two peptide in random state, close enough in parallel to each
other they also form parallel beta sheet structure ..
As the MD study is affected by initial arrangement.

I am interested How to Determine by Molecular Dynamics, Is  structure
favor Parallel
or Anti-parallel state ?  also the energy difference in two,
parallel  and anti-parallel 

Please give me some some valuable suggestion and method to solve my query.

Thank you in advance


Have a nice day
With Best Wishes and Regards
Ramadavid
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[gmx-users] About lipid simulation npt.mdp

2012-07-09 Thread rama david

Hi Gromacs friends,

I am trying to  reproduced the result of article  ¨Antimicrobial
peptide in Action¨
Published in JACS, 2006,128, 12156-12161, doi no = 10.1021/ja062927q

As per article they used two conditions,

1. Stress free ( Lateral  Tension = 0)
2. Stress condition ( Lateral  tension = 20 mNm/m)

parameter for simulation as follow,

Weakly coupled temp 323 k ( Coupling time = 0.1)
Weakly coupled press ( Coupling time = 0.5 Compressibility 5 e-5 bar -1)

Keep the P|| ( lateral press ) and  Pz( Perpendicular press ) same
P||  = Pz = 1 ,
Result will be stress free bilayer ( Lateral  Tension = 0).

For other condition of P||  =   -30  Pz = 1 , result in a lateral tension of
20 mNm/m

for stress free condition I made following npt.mdp
; Temperature coupling is on
tcoupl= Berendsen; More accurate thermostat
tc-grps= Protein DPPCSOL_CL; three coupling groups -
more accurate
tau_t= 0.10.10.1; time constant, in ps
ref_t= 323 323323; reference temperature,
one for each group, in K
; Pressure coupling is on
pcoupl=  Berendsen; Pressure coupling on in NPT
pcoupltype= semiisotropic; uniform scaling of x-y box
vectors, independent z
tau_p= 0.5; time constant, in ps
ref_p= 1.01.0; reference pressure, x-y, z (in bar)
compressibility = 5.0e-55.0e-5; isothermal compressibility, bar^-1


And for stress condition I made the following npt.mdp

; Temperature coupling is on
tcoupl= Berendsen; More accurate thermostat
tc-grps= Protein DPPCSOL_CL; three coupling groups -
more accurate
tau_t= 0.10.10.1; time constant, in ps
ref_t= 323 323323; reference temperature,
one for each group, in K
; Pressure coupling is on
pcoupl=  Berendsen; Pressure coupling on in NPT
pcoupltype= semiisotropic; uniform scaling of x-y box
vectors, independent z
tau_p= 0.5; time constant, in ps
ref_p=  -30.01.0; reference pressure, x-y,
z (in bar)
compressibility = 5.0e-55.0e-5; isothermal compressibility, bar^-1


Please help to make right npt.mdp from above  mention parameter.


I read the Gromacs manual for 4.5.4, Section 3.4 page no 33,
Surface tension coupling work with only Berendsen Press coupling.

Please , would you tell me how to calculate lateral surface tension from
P|| ( lateral press ) and  Pz( Perpendicular press )  ???
( Why to say  P||  =   -30  Pz = 1 , will give the teral tension of
20 mNm/m  ???)


Please give me the valuable suggestion in these regard

Thank you in advance.

Have a nice Day.
With best wishes and regards,


Rama David
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[gmx-users] About lipid simulation...

2012-07-09 Thread rama david

Hi Gromacs friends,

I am very novice to the lipid simulation study..
My problem may be very simple, But very imp to me to know it.

I am trying to  reproduced the result of article  ¨Antimicrobial
peptide in Action¨
Published in JACS, 2006,128, 12156-12161, doi no = 10.1021/ja062927q



As per article they used two conditions,

1. Stress free ( Lateral  Tension = 0)
2. Stress condition ( Lateral  tension = 20 mNm/m)

parameter for simulation as follow,

Weakly coupled temp 323 k ( Coupling time = 0.1)
Weakly coupled press ( Coupling time = 0.5 Compressibility 5 e-5 bar -1)

Keep the P|| ( lateral press ) and  Pz( Perpendicular press ) same
P||  = Pz = 1 ,
Result will be stress free bilayer ( Lateral  Tension = 0).

For other condition of P||  =   -30  Pz = 1 , result in a lateral tension of
20 mNm/m

for stress free condition I made following npt.mdp
; Temperature coupling is on
tcoupl= Berendsen; More accurate thermostat
tc-grps= Protein DPPCSOL_CL; three coupling groups -
more accurate
tau_t= 0.10.10.1; time constant, in ps
ref_t= 323 323323; reference temperature,
one for each group, in K
; Pressure coupling is on
pcoupl=  Berendsen; Pressure coupling on in NPT
pcoupltype= semiisotropic; uniform scaling of x-y box
vectors, independent z
tau_p= 0.5; time constant, in ps
ref_p= 1.01.0; reference pressure, x-y, z (in bar)
compressibility = 5.0e-55.0e-5; isothermal compressibility, bar^-1


And for stress condition I made the following npt.mdp

; Temperature coupling is on
tcoupl= Berendsen; More accurate thermostat
tc-grps= Protein DPPCSOL_CL; three coupling groups -
more accurate
tau_t= 0.10.10.1; time constant, in ps
ref_t= 323 323323; reference temperature,
one for each group, in K
; Pressure coupling is on
pcoupl=  Berendsen; Pressure coupling on in NPT
pcoupltype= semiisotropic; uniform scaling of x-y box
vectors, independent z
tau_p= 0.5; time constant, in ps
ref_p=  -30.01.0; reference pressure, x-y,
z (in bar)
compressibility = 5.0e-55.0e-5; isothermal compressibility, bar^-1


Please help to make right npt.mdp from above  mention parameter.


I read the Gromacs manual for 4.5.4, Section 3.4 page no 33,
Surface tension coupling work with only Berendsen Press coupling.

Please , would you tell me how to calculate lateral surface tension from
P|| ( lateral press ) and  Pz( Perpendicular press )  ???
( Why to say  P||  =   -30  Pz = 1 , will give the teral tension of
20 mNm/m  ???)


Please give me the valuable suggestion in these regard

Thank you in advance.

Have a nice Day.
With best wishes and regards,


Rama David
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Re: [gmx-users] genconf command

2012-07-17 Thread rama david

Dear cuong nguyen..
I think use following commands.

 Try editconf -rotate  for rotaion angle along axis
along these use -center  co-ordinate  if you want to place canter of
box at particular position

Try editconf -translate For translation along axis 



On Tue, Jul 17, 2012 at 2:07 PM, Mark Abraham mark.abra...@anu.edu.au wrote:
 On 17/07/2012 4:32 PM, cuong nguyen wrote:

 Dear Gmx-users,

 I created a box size 4 4 2 and named layer.gro. Then genconf was
 used to doulble this box:
 genconf -f layer.gro -o 2layers.gro -nbox 1 1 2 -dist 0 0 8
 However, the copied box has the same direction as the original box.
 Could you please help me to rotate 180 degrees the copied one?


 Start with genconf -h.

 Mark

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[gmx-users] Re: About lipid simulation...

2012-07-18 Thread rama david

 Hi Gromacs friends



 I read the Gromacs manual for 4.5.4, Section 3.4 page no 33,
 Surface tension coupling work with only Berendsen Press coupling.

 Please , would you tell me how to calculate lateral surface tension from
 P|| ( lateral press ) and  Pz( Perpendicular press )  ???
 ( Why to say  P||  =   -30  Pz = 1 , will give the teral tension of
 20 mNm/m  ???)




 I found out the way to calculate the lateral pressure..

  As per the article ..Biophysics Journal, October 1995, vol 65, page no
  1230.

  The formula as per article is

  Boundary lateral press =  1 -   ( Surface Tension / Thickness in Z
 dimension.)...


 ; Temperature coupling is on
 tcoupl= Berendsen; More accurate thermostat
 tc-grps= Protein DPPCSOL_CL; three coupling groups -
 more accurate
 tau_t= 0.10.10.1; time constant, in ps
 ref_t= 323 323323; reference temperature,
 one for each group, in K
 ; Pressure coupling is on
 pcoupl=  Berendsen; Pressure coupling on in NPT
 vectors, independent z
 tau_p= 0.5; time constant, in ps
 ref_p=  -30.01.0; reference pressure, x-y,z (in
 bar)

 compressibility = 5.0e-55.0e-5; isothermal compressibility, bar^-1
 pcoupltype= 

 What pcoupltype  shouild be used ???
 semiisotropic or Surface-tension 



 Please give me the valuable suggestion in these regard

 Thank you in advance.

 Have a nice Day.
 With best wishes and regards,


 Rama David


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[gmx-users] About Surface tension in lipid simulation.....

2012-07-18 Thread rama david

Hi Gromacs Friends,

I completed the Justin Protein KALP  - lipid tutorial ...

 I  want to simulate the DPPC lipid bilayer membrane under
 Stress condition ( Lateral  tension = 20 mNm/m)..

 For stress condition I made the following npt.mdp

; Temperature coupling is on
tcoupl   = Berendsen; More accurate thermostat
tc-grps  = Protein DPPCSOL_CL; three coupling groups
more accurate
tau_t= 0.10.10.1; time constant, in ps
ref_t = 323 323323; reference
temperature,one for each group,
; Pressure coupling is on
pcoupl   =  Berendsen; Pressure coupling on in NPT
pcoupltype  =  ??; uniform scaling of x-y box
vectors, independent z
tau_p   = 0.5; time constant, in ps
ref_p   =  -30.01.0; reference pressure, x-y,
z (in bar)
compressibility  = 5.0e-55.0e-5; isothermal compressibility, bar^-1


What pcoupl type Should be used Semisotropic or Surface tension.. and why???

Thank you in advance...

With Best Wishes and regards ,
Rama.
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[gmx-users] Gromacs installation

2012-07-30 Thread rama david

Hi GROMACS FRIENDS,
  I have dell T3500 precision, 64 bits, 6C workstation with fedora
operating system.
I want to install gromacs in parallel mode with mpi...
I am planning to performed Replica Exchange Molecular Dynamics ( REMD ).
As per REMD instruction
http://www.gromacs.org/Documentation/How-tos/REMD?highlight=remd,
GROMACS should not compile in threading.
I install open mpi with  command line yum -y install openmpi.
I found that fedora add/remove software package has gromacs 4.5.5
version that can be
easily installed by  command yum  ..
It  enlisted with  total 15 different packages : eg.. two packages..

1. GROMACS Open MPI binaries and libraries
2 . GROMACS OPEN MPI shared libraries

and a more..

Please can you tell me which packages I have to install so that I can
run GROMACS 4.5.5 in parallel to do REMD.


Thank you in advance
Have a nice day..


With Best Wishes and regards.
Rama David
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Re: [gmx-users] Gromacs installation

2012-07-30 Thread rama david

thank you for immediate reply...
Suppose, If I installed from Fedora software packages
How to check that  Gromacs installed in Parallel version and can
performed REMD



Thank you in Advance..
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Re: [gmx-users] Gromacs installation

2012-07-30 Thread rama david

Thank you M.ark..
I got following reply..

Fatal error :
mdrun -multi is not supported with thread library .Please compile
gromacs with MPI support.

I have to try to compile gromacs as per the webpage instructions...


With best wishes and regards..
Rama David..
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[gmx-users] About system requirement to gromacs

Hi Gromacs friends,

If anyone has a free time please reply to my Query..

Please accept my  SINCERE APOLOGY for my stupid query...
I have a limited knowledge about the computer hardware...

Is it possible to install Gromacs in parrallel mode in following system
in order to perform Replica Exchange Molecular Dynamics ( REMD )???...

1. Intel I5 processor, Dell Desktop.


and

2. Dell precision T 3500 Intel (R)Xeon (R)W3670 3.2 GHZ, 12M cache
  4.8 GT/s QPI, Tutbo, HT, 6C.

Is it possible to install gromacs-openmpi in both system to perform REMD
  or on only one ( Dell Precision T 3500 )...






With best Wishes and Regards...
Rama David
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Re: [gmx-users] About system requirement to gromacs

Thank you Mark for your Reply..

I install open-mpi through Ubuntu  software package ..
I know that these are not officially supported by the GROMACS team...


I made two different tpr file with the grompp command that has two
different temp..
( 300 K and 310 K) ..topol0.tpr topol1.tpr as your previous suggestion to me..

my command line was ..


mpirun mdrun_mpi -np 4  -multi 2 -replex 10


Fatal error:
The number of nodes (1) is not a multiple of the number of simulations (2)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

My Heart is Just a Muscle In a Cavity (F. Black)

Halting program mdrun_mpi

gcq#101: My Heart is Just a Muscle In a Cavity (F. Black)

--
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode -1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--






So what is wrong???

With best wishes and regards
Rama david
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Re: [gmx-users] About system requirement to gromacs

Thank you Mark for reply..

I run mdrun and mpirun with following command. I pasted output also..
Please help me to parse it..


1.   mdrun -v -deffnm topol1
2.   mpirun -np 4 mdrun -v -deffnm topol1


1.mdrun -v -deffnm topol1


step 30, will finish Wed Aug  1 16:49:28 2012
 Average load imbalance: 12.3 %
 Part of the total run time spent waiting due to load imbalance: 5.1 %

NOTE: 5.1 % performance was lost due to load imbalance
  in the domain decomposition.
  You might want to use dynamic load balancing (option -dlb.)


Parallel run - timing based on wallclock.

   NODE (s)   Real (s)  (%)
   Time:  2.035  2.035100.0
   (Mnbf/s)   (GFlops)   (ns/day)  (hour/ns)
Performance:109.127  5.744  2.632  9.117

gcq#98: You're About to Hurt Somebody (Jazzy Jeff)



2. mpirun -np 4 mdrun -v -deffnm topol1

Getting Loaded...
Reading file topol1.tpr, VERSION 4.5.5 (single precision)
Starting 4 threads
Starting 4 threads
Starting 4 threads
Starting 4 threads
Loaded with Money

Loaded with Money

Loaded with Money

Loaded with Money

Making 1D domain decomposition 4 x 1 x 1
Making 1D domain decomposition 4 x 1 x 1


Making 1D domain decomposition 4 x 1 x 1
Making 1D domain decomposition 4 x 1 x 1

starting mdrun 'Protein in water'
5 steps,100.0 ps.
starting mdrun 'Protein in water'
5 steps,100.0 ps.

starting mdrun 'Protein in water'
5 steps,100.0 ps.
starting mdrun 'Protein in water'
5 steps,100.0 ps.

NOTE: Turning on dynamic load balancing


NOTE: Turning on dynamic load balancing

step 0
NOTE: Turning on dynamic load balancing

step 100, will finish Wed Aug  1 19:36:10 2012vol 0.83  imb F  2% vol
0.84  imb step 200, will finish Wed Aug  1 19:32:37 2012vol 0.87  imb
F 16% vol 0.86  imb step 300, will finish Wed Aug  1 19:34:59 2012vol
0.88  imb F  4% vol 0.85  imb step 400, will finish Wed Aug  1
19:36:27 2012^Cmpirun: killing job...

--
mpirun noticed that process rank 0 with PID 4257 on node  VPCEB34EN
exited on signal 0 (Unknown signal 0).
--
4 total processes killed (some possibly by mpirun during cleanup)
mpirun: clean termination accomplished




As you can also see the mdun command estimate to complete Aug  1 16:49:28 2012
while mpirun taking the time Wed Aug  1 19:36:10 2012vol

Mpirun command taking more time...

so from above output I can  guess In mpirun 4 processor are used


Sorry if I take any wrong meaning from output..

Thank you for giving your valuable time..


With best wishes and regards

Rama David
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Re: [gmx-users] About system requirement to gromacs

Thank you for reply and your suggestion..

As I mentioned earlier I installed Gromacs-openmpi 4.5.5  from Ubuntu
software package manager

So I want to just check is it performing REMD or  not???

So as per previous suggestion of Mark ...
I made two tpr file that has two different temp 300 k and 310
k..topol0.tpr and topol1.tpr  respectively


I used command line

 mpirun -c 4   mdrun_mpi  -v -multi 2 -replex 10

output as follow.


node 0 par_fn 'topol0.tpr'
node 0 par_fn 'topol1.tpr'
node 0 par_fn 'traj1.trr'
node 0 par_fn 'traj1.xtc'
node 0 par_fn 'state1.cpt'
node 0 par_fn 'state1.cpt'
node 0 par_fn 'confout1.gro'
node 0 par_fn 'ener1.edr'
node 0 par_fn 'traj0.trr'
node 0 par_fn 'md1.log'
log
node 0 par_fn 'traj0.xtc'
node 0 par_fn 'dhdl1.xvg'
node 0 par_fn 'field1.xvg'
node 0 par_fn 'state0.cpt'
node 0 par_fn 'rerun1.xtc'
node 0 par_fn 'tpi1.xvg'
node 0 par_fn 'tpidist1.xvg'
node 0 par_fn 'state0.cpt'
node 0 par_fn 'sam1.edo'
node 0 par_fn 'confout0.gro'
node 0 par_fn 'bam1.gct'
node 0 par_fn 'gct1.xvg'
node 0 par_fn 'ener0.edr'
node 0 par_fn 'deviatie1.xvg'
node 0 par_fn 'runaver1.xvg'
node 0 par_fn 'md0.log'
node 0 par_fn 'pullx1.xvg'
node 0 par_fn 'pullf1.xvg'
node 0 par_fn 'nm1.mtx'
log
node 0 par_fn 'dipole1.ndx'
node 0 par_fn 'dhdl0.xvg'

Back Off! I just backed up md1.log to ./#md1.log.4#
Getting Loaded...
Reading file topol1.tpr, VERSION 4.5.5 (single precision)
node 0 par_fn 'field0.xvg'
node 0 par_fn 'rerun0.xtc'
node 0 par_fn 'tpi0.xvg'
node 0 par_fn 'tpidist0.xvg'
node 0 par_fn 'sam0.edo'
node 0 par_fn 'bam0.gct'
node 0 par_fn 'gct0.xvg'
node 0 par_fn 'deviatie0.xvg'
node 0 par_fn 'runaver0.xvg'
node 0 par_fn 'pullx0.xvg'
node 0 par_fn 'pullf0.xvg'
node 0 par_fn 'nm0.mtx'
node 0 par_fn 'dipole0.ndx'

Back Off! I just backed up md0.log to ./#md0.log.4#
Getting Loaded...
Reading file topol0.tpr, VERSION 4.5.5 (single precision)
Loaded with Money

Loaded with Money

Making 1D domain decomposition 2 x 1 x 1

Back Off! I just backed up traj0.trr to ./#traj0.trr.4#

Back Off! I just backed up ener0.edr to ./#ener0.edr.4#
Making 1D domain decomposition 2 x 1 x 1

Back Off! I just backed up traj1.trr to ./#traj1.trr.4#

Back Off! I just backed up ener1.edr to ./#ener1.edr.4#

---
Program mdrun_mpi, VERSION 4.5.5
Source code file: /build/buildd/gromacs-4.5.5/src/kernel/repl_ex.c, line: 177

Fatal error:
The properties of the 2 systems are all the same, there is nothing to exchange
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

I Do It All the Time (Magnapop)


---
Program mdrun_mpi, VERSION 4.5.5
Source code file: /build/buildd/gromacs-4.5.5/src/kernel/repl_ex.c, line: 177

Fatal error:
The properties of the 2 systems are all the same, there is nothing to exchange
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

I Do It All the Time (Magnapop)

Error on node 2, will try to stop all the nodes
Halting parallel program mdrun_mpi on CPU 2 out of 4
Error on node 0, will try to stop all the nodes
Halting parallel program mdrun_mpi on CPU 0 out of 4

gcq#197: I Do It All the Time (Magnapop)


gcq#197: I Do It All the Time (Magnapop)

--
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode -1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--
--
mpirun has exited due to process rank 0 with PID 9919 on
node VPCEB34EN exiting without calling finalize. This may
have caused other processes in the application to be
terminated by signals sent by mpirun (as reported here).
--
[VPCEB34EN:09918] 1 more process has sent help message
help-mpi-api.txt / mpi-abort
[VPCEB34EN:09918] Set MCA parameter orte_base_help_aggregate to 0 to
see all help / error messag



Thanks a lot for hearing my problem

So from above output is it able to perform REMD or not ?
Is the gromacs installation  on my system is right for open-mpi


With Best Wishes and regards

Rama david
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[gmx-users] Gromacs configuration error....configure error : cannot compute sizeof ( off_t)...

2012-08-07 Thread rama david

Hi Gromacs Friends,

I am trying to install gromacs 4.5.4  in parallel operating system fedora 17
I am using dell T 3500 precision , 6C.

I downloaded openmppi-1.6
Command line to install
   ./configure --prefix=/usr/local
 make all install

For fftw 3.3.2 installation command line was .

./configure --enable-float
make
make install

To Gromacs I wrote..
./configure --enable-mpi --with-fft=fftw3 --program-suffix=_mpi


System reply with
  configure error : cannot compute sizeof ( off_t)...

config .log show following error...It very big..I am pesting only a
small part...

Please tell me the reason for such error ...?? And how to overcome these???
.
.
.
.
.
.
configure:5529: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME gromacs
| #define PACKAGE_TARNAME gromacs
| #define PACKAGE_VERSION 4.5.4
| #define PACKAGE_STRING gromacs 4.5.4
| #define PACKAGE_BUGREPORT gmx-users@gromacs.org
| #define PACKAGE_URL 
| #define PACKAGE gromacs
| #define VERSION 4.5.4
| #define GMX_SOFTWARE_INVSQRT /**/
| #define GMX_QMMM_GAUSSIAN /**/
| #define GMX_QMMM_ORCA /**/
| #define BUILD_TIME Tue Aug  7 10:46:37 IST 2012
| #define BUILD_MACHINE Linux 3.5.0-2.fc17.x86_64 x86_64
| #define GMX_MPI /**/
| #define GMX_LIB_MPI /**/
| #define MPI_IN_PLACE_EXISTS /**/
| /* end confdefs.h.  */
|
| #if defined __QK_USER__
| #else
| #error not catamount
| #endif
|
| int
| main ()
| {
|
|   ;
|   return 0;
| }
configure:5551: result: no
configure:6229: checking how to run the C preprocessor
configure:6260: mpicc -E -I/usr/local/lib conftest.c
configure:6260: $? = 0
configure:6274: mpicc -E -I/usr/local/lib conftest.c
conftest.c:22:28: fatal error: ac_nonexistent.h: No such file or directory
compilation terminated.
configure:6274: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME gromacs
| #define PACKAGE_TARNAME gromacs
| #define PACKAGE_VERSION 4.5.4
| #define PACKAGE_STRING gromacs 4.5.4
| #define PACKAGE_BUGREPORT gmx-users@gromacs.org
| #define PACKAGE_URL 
| #define PACKAGE gromacs
| #define VERSION 4.5.4
| #define GMX_SOFTWARE_INVSQRT /**/
| #define GMX_QMMM_GAUSSIAN /**/
| #define GMX_QMMM_ORCA /**/
| #define BUILD_TIME Tue Aug  7 10:46:37 IST 2012
| #define BUILD_USER prashant@prashant
| #define BUILD_MACHINE Linux 3.5.0-2.fc17.x86_64 x86_64
| #define GMX_MPI /**/
| #define GMX_LIB_MPI /**/
| #define MPI_IN_PLACE_EXISTS /**/
| #define F77_OR_C_FUNC(name,NAME) name
| #define F77_OR_C_FUNC_(name,NAME) name
| /* end confdefs.h.  */
| #include ac_nonexistent.h
configure:6299: result: mpicc -E
configure:6319: mpicc -E -I/usr/local/lib conftest.c
configure:6319: $? = 0
configure:6333: mpicc -E -I/usr/local/lib conftest.c
conftest.c:22:28: fatal error: ac_nonexistent.h: No such file or directory
compilation terminated.
configure:6333: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME gromacs
| #define PACKAGE_TARNAME gromacs
| #define PACKAGE_VERSION 4.5.4
| #define PACKAGE_STRING gromacs 4.5.4
| #define PACKAGE_BUGREPORT gmx-users@gromacs.org
| #define PACKAGE_URL 
| #define PACKAGE gromacs
| #define VERSION 4.5.4
| #define GMX_SOFTWARE_INVSQRT /**/
| #define GMX_QMMM_GAUSSIAN /**/
| #define GMX_QMMM_ORCA /**/
| #define BUILD_TIME Tue Aug  7 10:46:37 IST 2012
| #define BUILD_USER prashant@prashant
| #define BUILD_MACHINE Linux 3.5.0-2.fc17.x86_64 x86_64
| #define GMX_MPI /**/
| #define GMX_LIB_MPI /**/
| #define MPI_IN_PLACE_EXISTS /**/
| #define F77_OR_C_FUNC(name,NAME) name
| #define F77_OR_C_FUNC_(name,NAME) name
| /* end confdefs.h.  */
| #include ac_nonexistent.h
configure:6362: checking for grep that handles long lines and -e
configure:6420: result: /usr/bin/grep
configure:6425: checking for egrep
configure:6487: result: /usr/bin/grep -E
configure:6492: checking whether ln -s works
configure:6496: result: yes
configure:6895: checking whether mpicc accepts -O3
configure:6913: result: yes
configure:7193: checking whether mpicc accepts -msse2
configure:7211: result: yes
configure:7225: checking whether mpicc accepts -funroll-all-loops
configure:7243: result: yes
configure:7255: checking whether mpicc accepts -std=gnu99
configure:7273: result: yes
configure:7288: checking whether mpicc accepts -fexcess-precision=fast
configure:7306: result: yes
configure:7347: checking whether mpicc accepts  -O3
-fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2
-funroll-all-loops -std=gnu99 -fexcess-precision=fast
configure:7365: result: yes
configure:8089: checking whether byte ordering is bigendian
configure:8104: mpicc -c  -O3 -fomit-frame-pointer -finline-functions
-Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99
-fexcess-precision=fast -I/usr/local/lib conftest.c 5
conftest.c:23:9: error: unknown type name 'not'
conftest.c:23:15: error: expected '=', ',', ';', 'asm' or
'__attribute__' before 'universal'
conftest.c:23:15: error: unknown type name 'universal'
configure:8104: $? = 1
configure: failed program was:
| /* confdefs.h */
|

Re: [gmx-users] Gromacs configuration error....configure error : cannot compute sizeof ( off_t)...

2012-08-08 Thread rama david

 directory `/opt/gromacs-4.5.4/src/kernel'
(cd ./src/kernel  make install-mdrun ; exit 0)
make[1]: Entering directory `/opt/gromacs-4.5.4/src/kernel'
/bin/sh ../../config/mkinstalldirs /opt/gmx_4.5.4/bin
if test -f mdrun; then \
  f=`echo mdrun|sed 's/$//;s$_mpi;s/$//'`; \
  echo   /bin/sh ../../libtool  --mode=install /usr/bin/install -c
mdrun /opt/gmx_4.5.4/bin/$f; \
   /bin/sh ../../libtool  --mode=install /usr/bin/install -c mdrun
/opt/gmx_4.5.4/bin/$f; \
else :; fi
  /bin/sh ../../libtool  --mode=install /usr/bin/install -c mdrun
/opt/gmx_4.5.4/bin/mdrun_mpi
/usr/bin/install -c mdrun /opt/gmx_4.5.4/bin/mdrun_mpi
make[1]: Leaving directory `/opt/gromacs-4.5.4/src/kernel'
[root@prashant gromacs-4.5.4]# make links
cd /opt/gmx_4.5.4/bin  programs=`ls`  cd /usr/local/bin  \
for i in $programs; do \
   (test ! -f $i  ln -s /opt/gmx_4.5.4/bin/$i . ; exit 0); \
done


When I am giving the command
pdb2gmx_mpi
pdb2gmx_mpi: error while loading shared libraries: libmpi.so.1: cannot
open shared object file: No such file or directory


I have a small experience in linux only, That why I may be missing or
done something wrong???
So please tell me where is the problem 

Thank you in advane..

With Best wishes and regards,
Rama david.
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Re: [gmx-users] checkpoint file

Hi  Juliette ,

If your data is more and because of that may be  -append not support you.

Then these may be help you ..

mdrun -v -deffnm use different name than previous -s your tpr file
-cpi cpt

See carefully the output and check the time  at which the run
start..Is the  starting time point matches your crash point.

lastly when run complete, use trajcat ( catenate two trajectory),
catenate two trajectory...(previous and latest)

you can also catenate edr file..

So 1st make clear that why run crash??? If no abnormality then proceed
further...

These is the way I tackle my crash run on Gromacs 4.5.4


With best wishes and regards,
Rama David
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Re: [gmx-users] grommp warning

Dear shima and Justin,

These error is come on Gromacs 4.5.5 at the time of NPT if
refcoord_scaling option not used..

But it is not come on Gromacs 4.5.4 when you not use  refcoord_scaling
option at npt

Is any one else has same experience?
I really surprised by my observation  

With best wishes and regards
Rama David..
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Re: [gmx-users] grommp warning

Justin,
Thank you for your reply,

I check the manual but it is giving only small information..

I would be greatly thankfull to you if you shed some light on
these option ...

With best wishes and regards
Rama David
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Re: [gmx-users] grommp warning

Hi Justin ,

Thank you for immediate reply and providing the link.

But I am wonder for following things...

For protein simulation in your lysozyme tutorial we use
refcoord_scaling = com
In lipid tutorial also same one..

So Is there are any case when to use
refcoord_scaling no or all .??

Is there any way to find out which option to use when

How all the things going to affect the result

I goes trough archive but not find satisfactory answer...
I am looking for clear and simple explanation...


Thank you in advance..

With Best wishes and regards
Rama david
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Re: [gmx-users] grommp warning

2012-08-15 Thread rama david

Thank you Mark for reply.

as you said ...
Depends whether rigidity or scaling make more sense in your model of
real physics, which depends what's in your system.

My system is generally consist of proteins or peptides ( single ,
double or many)..

I am using option com Is it right

As per your answer in these archieve...
http://lists.gromacs.org/pipermail/gmx-users/2011-November/065815.html


Under NPT the box size changes each step. You are using position
restraints to a pre-defined set of reference coordinates. This option
allows you to choose how those *reference coordinates* should change
when the box size changes (respectively do not scale them at all, scale
them all, or scale their COM but leave their internal geometry fixed).
Position restraints are then applied using the updated reference
coordinates.


In some archives I found if any one used freeze group
suggested to use refcoord_scaling = no


When we applied position restrain, the position of backbone atom is restrained..
I make my assumption as like follow..
No = no scalling in position of atoms.(system maintain rigidity).
all  = the system bcome flexible

com= ? ( scalling com means changing com co-ordinates or something else)




I get confused


Please accept my apology for stupid question
Please help to come out through the confusion.

With best wishes and regards

Rama david
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Re: [gmx-users] my VMD

2012-08-16 Thread rama david

Hi
do the following ..

open the trajectory in tthe molecule not as seperate molecule..

As example you havre md.gro and md.xtc files..

file == new molecule

load files for md.pdb   open it in vmd ..
then be sure that load files for : sould have the file name for which
you want to see treajectory...here md.gro
through browse open the md.xtc then load it..

With best wishes aned regards..

Rama david


On Wed, Aug 15, 2012 at 3:27 PM, Acoot Brett acootbr...@yahoo.com wrote:
 Dear All,

 I just installed a VMD. And then I load a gro file and a xtc file from a 
 simulation. The bar in the VMD Main window continuously moves, however the 
 protein molecule in the OpenGL Display window does not move.

 Will you please tell me what is the problem, or how can see the whole 
 simulation?

 Cheers,

 Acoot
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Re: [gmx-users] my VMD

2012-08-16 Thread rama david

Sorry md.pdb/md.gro

On Thu, Aug 16, 2012 at 11:34 AM, rama david ramadavidgr...@gmail.com wrote:
 Hi
 do the following ..

 open the trajectory in tthe molecule not as seperate molecule..

 As example you havre md.gro and md.xtc files..

 file == new molecule

 load files for md.pdb   open it in vmd ..
 then be sure that load files for : sould have the file name for which
 you want to see treajectory...here md.gro
 through browse open the md.xtc then load it..

 With best wishes aned regards..

 Rama david


 On Wed, Aug 15, 2012 at 3:27 PM, Acoot Brett acootbr...@yahoo.com wrote:
 Dear All,

 I just installed a VMD. And then I load a gro file and a xtc file from a 
 simulation. The bar in the VMD Main window continuously moves, however the 
 protein molecule in the OpenGL Display window does not move.

 Will you please tell me what is the problem, or how can see the whole 
 simulation?

 Cheers,

 Acoot
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Re: [gmx-users] on tpbconv

2012-09-30 Thread rama david

Yes it will work ..
Just at the time of mdrun add -cpi cpt ( prvious cpt file )

With best wishes and regards..!!

On Sun, Sep 30, 2012 at 8:48 AM, Acoot Brett acootbr...@yahoo.com wrote:

 Dear All,

 for my original MD, based on mdp file the total time is 500 ps. After it
 finished,  I have decided to extend the MD run to 2.5 ns.

 I think the following command should be used:

 tpbconv -s original500ps.tpr -extend 2000 -o md-0.5ns-to-2.5ns.tpr


 But as for in the original mdp file the total time is 500 ps,is the
 -extend 2000 workable in the tpbconv -s original500ps.tpr -extend 2000
 -o md-0.5ns-to-2.5ns.tpr? Do I need to change the total time in the
 original mdp file from 500 ps to 2000 ps or a time period longer than 2000
 ps, after the original 500 pd finished, in order to make tpbconv -s
 original500ps.tpr -extend 2000 -o md-0.5ns-to-2.5ns.tpr workable?

 I am looking forward to getting your reply.

 Cheers,

 Acoot
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Re: [gmx-users] Calculate Density with respect to time...

2012-09-30 Thread rama david

Thank you for your immediate reply..

I need the xvg graph that will tell me the density of water in between the
protein with respect to time .
g_densmap not give such out put..

Sol please would you tell me  how to do it ???

How to select the Sol that  are only in between the protein ??


Thank you in advance..


With best wishes and regards

Rama David
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Re: [gmx-users] A snapshot at a particular time frame

2012-10-01 Thread rama david

Dear Ravi
   Use trjconv  -dump ... ( time in ps)

With Best wishes and regards
Rama david.

On Mon, Oct 1, 2012 at 11:15 AM, Ravi Kumar Venkatraman 
ravikumarvenkatra...@gmail.com wrote:

 Dear All,
  How to get a snapshot at a particular time frame from the MDS
 run.
 Thank you

 *With Regards,
 Ravi Kumar Venkatraman,
 IPC Dept., IISc,
 Bangalore, INDIA.

 +91-9686933963.*
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Re: [gmx-users] Density measurment

2012-10-02 Thread rama david

Thank you Justin for your reply ,

I tried g_density again after your reply. But I found that
it give density with respect to box dimension and not to time.

g_densmap have xpm output and no the xvg ( I need density or no of water
molecule present in between two peptides with respect to the time )..

Please, would you tell me another way to solve these problem..??

Thank you in advance

Have a nice day.
Rama David

On Tue, Oct 2, 2012 at 8:28 PM, Justin Lemkul jalem...@vt.edu wrote:

On 10/2/12 7:07 AM, rama david wrote:

Hi Gromacs Users,

I did simulation of two random coil peptides for 100ns.
after 70 ns these peptide get converted to anti parallel beta sheet
structure.
I am interested to see the water density in between these peptideswith
respect to time change
and also the no of water molecule between the peptide with respect to
time.
And at the same time the distance between the peptide..
I need these information in xvg graph.

I found out the distance between peptide by g_mindist
but I not found the appropriate way to calculate density of water with
respect to time
between two peptides..

I used g_density but it not gave me the information as per my need.

There are a variety of options in g_density that might work, like changing
the direction along which the box is sliced, the interval of time examined,
etc. I can envision this working quite well. g_densmap can do similar
functions, and g_rdf can probably provide you with some useful information
as well.

-Justin

--
==**==

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

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Re: [gmx-users] Problem with the installation of Gromacs 4-5.5

2012-10-03 Thread rama david

Hi Deepak,

Is the gromacs is in your path??

Please mention your operating system..

With best wishes and Regards,
rama david

On Thu, Oct 4, 2012 at 11:07 AM, Deepak Ojha alwaysinthem...@gmail.comwrote:

 Dear All
 I want to use Amber force field in Gromacs therefore I installed the
 latest version of Gromacs and
 installed accordingly as per as the instructions given in INSTALL.automake
 file.
 ./configure
 make
 make install

 It works fine and shows the message that installation is complete but
 none of the commands like
 pdb2gmx,mdrun works.Even the luck does not works which is meant to
 test the installation of gromacs.
 What is the issue with the installation.Please help me resolve it.

 Regards
 DeepaK Ojha
 School Of Chemistry

 Selfishness is not living as one wishes to live, it is asking others
 to live as one wishes to live
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Re: [gmx-users] Interaction study for peptide-receptor..

thank you Justin for reply.

I dont know about long range interactions.
But as I freeze the group I think it will improve my computational speed.
So is there any way to find out or decide which group should be
freeze, and which group should affect my interaction most probably??

Should I do Essential Dynamics ??? or Principle component analysis ???

Would you suggest me any general protocol for such work??

Thank you in Advance

With Best Wishes and regards.
Rama David

On Thu, Oct 4, 2012 at 3:57 PM, Justin Lemkul jalem...@vt.edu wrote:

On 10/4/12 2:01 AM, rama david wrote:

Hi gromacs Friends,
I want to do peptide-receptor ( Protein) interaction
study.Receptor consist a single chain.
Peptide is made up of 4 amino acids. I know the interaction pattern of
peptide and receptor.
I plan to mutate single residue each at a time and run 4 simulation .
So I will have the 4 different simulation that contain the mutated
residues
and the wild one.

Then afterward from the interaction energy I want to select the peptide
which is showing
stronger interaction than others.

As mention I know the binding site, If I freeze the remaining portion in
receptor
that not involved in binding , Is it going to affect my screening process
???

Potentially. Do you know that the binding interactions and the mutations
will only perturb local residues? Do you know that there are no long-range
motions to be considered?

I think you gain very little by freezing portions of the system, and risk
more than you gain.

-Justin

--
==**==

Re: [gmx-users] Interaction study for peptide-receptor..

Hi francesco,

Thank you For reply.
I did docking but the result are not so impressive.
I used vina and autodock.
I also did virtual screening in autodock but the result are not upto the
mark.

Is the freezing of group can affect my system?? How much efficiency I get
by these work??
As these group are going to freeze in four simulation so if it affect one
ligand it  affect other
ligand also.

I read article that did the work like me ,
they sliced the binding residues and  used the inert solid sphere to
support binding residues
instead of the freezing group other group.

I think both way should have same effect..Am I right or wrong??

If you have any other way please suggest it..

With best wishes and regards
Rama david


On Thu, Oct 4, 2012 at 5:07 PM, francesco oteri
francesco.ot...@gmail.comwrote:

 Hi,
 as far as I know, freezing just set velocities to 0 so you gain nothing
 freezing atoms.

 By the way, have you tried docking? It takes into account multiple
 conformation and
 orientation of the peptide and, depending upon the implemented algorithm,
 also
 protein sidechain orientation.

 Francesco


 2012/10/4 rama david ramadavidgr...@gmail.com

  thank you Justin for reply.
 
  I dont know about long range interactions.
  But as I freeze the group I think it will improve my computational speed.
  So is there any way to find out or decide which group should be
  freeze, and which group should affect my interaction most probably??
 
  Should I do Essential Dynamics ??? or Principle component analysis ???
 
  Would you suggest me any general protocol for such work??
 
  Thank you in Advance
 
 
  With Best Wishes and regards.
  Rama David
 
  On Thu, Oct 4, 2012 at 3:57 PM, Justin Lemkul jalem...@vt.edu wrote:
 
  
  
   On 10/4/12 2:01 AM, rama david wrote:
  
   Hi gromacs Friends,
I want to do peptide-receptor ( Protein) interaction
   study.Receptor consist a single chain.
   Peptide is made up  of  4 amino acids. I know the interaction pattern
 of
   peptide and receptor.
   I plan to mutate single residue each at a time and  run 4 simulation .
   So I will have the 4 different simulation that contain the mutated
   residues
   and the wild one.
  
  
   Then afterward from the interaction energy I want to select the
 peptide
   which is showing
   stronger interaction than others.
  
   As  mention I know the binding site, If I freeze the remaining portion
  in
   receptor
   that not involved in binding , Is it going to affect my screening
  process
   ???
  
  
   Potentially.  Do you know that the binding interactions and the
 mutations
   will only perturb local residues?  Do you know that there are no
  long-range
   motions to be considered?
  
   I think you gain very little by freezing portions of the system, and
 risk
   more than you gain.
  
   -Justin
  
   --
   ==**==
  
   Justin A. Lemkul, Ph.D.
   Research Scientist
   Department of Biochemistry
   Virginia Tech
   Blacksburg, VA
   jalemkul[at]vt.edu | (540) 231-9080
   http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
  http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
  
   ==**==
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 Cordiali saluti, Dr.Oteri Francesco
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Re: [gmx-users] Interaction study for peptide-receptor..

Thank you justin and franscisco,
I have practical data that claim that only a particular residue that is c
terminal residue  is
involve in binding.
  but when I generate the docking data other residues most of the time
comes to play.
I know the binding of natural ligand ( peptide ) and the position.
so I think if I mutate only these residue and simulate the system I will
get the
structure that is more active. In natural ligand the C terminal is playing
important role.


With simulation i will find interaction energy.
  That will tell me about binding affinity  ( Hope so )
These is my basic idea.

Is any other way to do the same thing..

With best wishes and regards
Rama David


On Thu, Oct 4, 2012 at 5:47 PM, francesco oteri
francesco.ot...@gmail.comwrote:

 2012/10/4 rama david ramadavidgr...@gmail.com

  Hi francesco,
 
  Thank you For reply.
  I did docking but the result are not so impressive.
 

 What does it mean not so impressive? I mean, do you have experimental
 data
 and the comparison with docking doesn't agree with experiments? Have you
 generated
 a sufficient number of complexes (say 100 or more)?

 I used vina and autodock.
  I also did virtual screening in autodock but the result are not upto the
  mark.
 
  Is the freezing of group can affect my system?? How much efficiency I get
  by these work??
 

 It will change a lot the dynamics of your system and I don't think
 calculations
 will be more efficient!


  As these group are going to freeze in four simulation so if it affect one
  ligand it  affect other
  ligand also.
 
  I read article that did the work like me ,
  they sliced the binding residues and  used the inert solid sphere to
  support binding residues
  instead of the freezing group other group.
 
  I think both way should have same effect..Am I right or wrong??
 
  If you have any other way please suggest it..
 

 If you already have docking complexes, you can pick up one complex for each
 peptide, to run an MD, or Free Energy  calculations.
 It strongly depends by the experimentale data you have and what is the
 target
 of your work.


 
  With best wishes and regards
  Rama david
 
 
  On Thu, Oct 4, 2012 at 5:07 PM, francesco oteri
  francesco.ot...@gmail.comwrote:
 
   Hi,
   as far as I know, freezing just set velocities to 0 so you gain nothing
   freezing atoms.
  
   By the way, have you tried docking? It takes into account multiple
   conformation and
   orientation of the peptide and, depending upon the implemented
 algorithm,
   also
   protein sidechain orientation.
  
   Francesco
  
  
   2012/10/4 rama david ramadavidgr...@gmail.com
  
thank you Justin for reply.
   
I dont know about long range interactions.
But as I freeze the group I think it will improve my computational
  speed.
So is there any way to find out or decide which group should be
freeze, and which group should affect my interaction most probably??
   
Should I do Essential Dynamics ??? or Principle component analysis
 ???
   
Would you suggest me any general protocol for such work??
   
Thank you in Advance
   
   
With Best Wishes and regards.
Rama David
   
On Thu, Oct 4, 2012 at 3:57 PM, Justin Lemkul jalem...@vt.edu
 wrote:
   


 On 10/4/12 2:01 AM, rama david wrote:

 Hi gromacs Friends,
  I want to do peptide-receptor ( Protein) interaction
 study.Receptor consist a single chain.
 Peptide is made up  of  4 amino acids. I know the interaction
  pattern
   of
 peptide and receptor.
 I plan to mutate single residue each at a time and  run 4
  simulation .
 So I will have the 4 different simulation that contain the mutated
 residues
 and the wild one.


 Then afterward from the interaction energy I want to select the
   peptide
 which is showing
 stronger interaction than others.

 As  mention I know the binding site, If I freeze the remaining
  portion
in
 receptor
 that not involved in binding , Is it going to affect my screening
process
 ???


 Potentially.  Do you know that the binding interactions and the
   mutations
 will only perturb local residues?  Do you know that there are no
long-range
 motions to be considered?

 I think you gain very little by freezing portions of the system,
 and
   risk
 more than you gain.

 -Justin

 --
 ==**==

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

 ==**==
 --
 gmx-users mailing listgmx-users@gromacs.org
 http://lists.gromacs.org/**mailman/listinfo/gmx-users
http://lists.gromacs.org/mailman

Re: [gmx-users] Interaction study for peptide-receptor..

Thank you  for reply,
 I read the recently published article in Biochemistry.
They worked on the same receptor that I am working.
( as I mention in my previous mail)
They used NAMD software and I am using gromacs.
They sliced the  receptor binding site and used the the solid support
to the binding site and did simulation.
   So if I freeze  the group is it will ok ??
Is it possible in gromacs to fix the residue on solid immobilized surface.
If it is how to do it??

my question is How to decide which group are remove and which group should
keep in simulation.

thank you in advance
Thank you for giving your valuable time and advice to me.

With best wishes and regards,
Rama david






On Thu, Oct 4, 2012 at 6:11 PM, Thomas Evangelidis teva...@gmail.comwrote:

 I don't think AutoDock and Vina are suitable for peptide docking. I would
 first try the FlexPepDocking module of Rosetta which does ab initio folding
 of the peptide on the receptor, while moving the side-chains of the protein
 but leaves its backbone intact. Rosetta implements a knowledge-based
 scoring, which has been specifically designed for this task and is as fast
 as Vina or AutoDock.

 I would first do that and if I wouldn't get any reasonable results then I
 would move to MD starting from the top scored protein-peptide complexes
 created by Rosetta.

 Thomas


 On 4 October 2012 15:08, rama david ramadavidgr...@gmail.com wrote:

  Hi francesco,
 
  Thank you For reply.
  I did docking but the result are not so impressive.
  I used vina and autodock.
  I also did virtual screening in autodock but the result are not upto the
  mark.
 
  Is the freezing of group can affect my system?? How much efficiency I get
  by these work??
  As these group are going to freeze in four simulation so if it affect one
  ligand it  affect other
  ligand also.
 
  I read article that did the work like me ,
  they sliced the binding residues and  used the inert solid sphere to
  support binding residues
  instead of the freezing group other group.
 
  I think both way should have same effect..Am I right or wrong??
 
  If you have any other way please suggest it..
 
  With best wishes and regards
  Rama david
 
 
  On Thu, Oct 4, 2012 at 5:07 PM, francesco oteri
  francesco.ot...@gmail.comwrote:
 
   Hi,
   as far as I know, freezing just set velocities to 0 so you gain nothing
   freezing atoms.
  
   By the way, have you tried docking? It takes into account multiple
   conformation and
   orientation of the peptide and, depending upon the implemented
 algorithm,
   also
   protein sidechain orientation.
  
   Francesco
  
  
   2012/10/4 rama david ramadavidgr...@gmail.com
  
thank you Justin for reply.
   
I dont know about long range interactions.
But as I freeze the group I think it will improve my computational
  speed.
So is there any way to find out or decide which group should be
freeze, and which group should affect my interaction most probably??
   
Should I do Essential Dynamics ??? or Principle component analysis
 ???
   
Would you suggest me any general protocol for such work??
   
Thank you in Advance
   
   
With Best Wishes and regards.
Rama David
   
On Thu, Oct 4, 2012 at 3:57 PM, Justin Lemkul jalem...@vt.edu
 wrote:
   


 On 10/4/12 2:01 AM, rama david wrote:

 Hi gromacs Friends,
  I want to do peptide-receptor ( Protein) interaction
 study.Receptor consist a single chain.
 Peptide is made up  of  4 amino acids. I know the interaction
  pattern
   of
 peptide and receptor.
 I plan to mutate single residue each at a time and  run 4
  simulation .
 So I will have the 4 different simulation that contain the mutated
 residues
 and the wild one.


 Then afterward from the interaction energy I want to select the
   peptide
 which is showing
 stronger interaction than others.

 As  mention I know the binding site, If I freeze the remaining
  portion
in
 receptor
 that not involved in binding , Is it going to affect my screening
process
 ???


 Potentially.  Do you know that the binding interactions and the
   mutations
 will only perturb local residues?  Do you know that there are no
long-range
 motions to be considered?

 I think you gain very little by freezing portions of the system,
 and
   risk
 more than you gain.

 -Justin

 --
 ==**==

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

 ==**==
 --
 gmx-users mailing listgmx-users@gromacs.org
 http://lists.gromacs.org/**mailman

Re: [gmx-users] Interaction energy calculation..

Hi justin,
I completed the simulation ,
Now I want to use the selected residues of protein and ligand.
How to do it

Would you explain me in detail??

With best wishes and regards,
Rama david.


On Fri, Oct 5, 2012 at 3:40 PM, Justin Lemkul jalem...@vt.edu wrote:



 On 10/5/12 5:49 AM, rama david wrote:

 Hi Friends,

 I want to study the interaction energy between the selected residues of
 protein and ligand.

 ( Non-bonded energy should include : vanderwall and electrostatics)

 How to do it???


 This is what the energygrps keyword in the .mdp file is for.  Beware the
 interpretation and utility of these quantities.

 -Justin

 --
 ==**==

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

Hi justin,
thank you for reply.

With best wishes and regards
Rama david.



On Fri, Oct 5, 2012 at 4:07 PM, Justin Lemkul jalem...@vt.edu wrote:



 On 10/5/12 6:15 AM, rama david wrote:

 Hi justin,
 I completed the simulation ,
 Now I want to use the selected residues of protein and ligand.
 How to do it

 Would you explain me in detail??


 Create a new .tpr file from an .mdp file with suitable energygrps.  Use
 mdrun -rerun to recalculate energies.


 -Justin

 --
 ==**==

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

Thank you for your Help.

I did the following tc-groups

tcoupl= V-rescale; modified Berendsen thermostat
tc-grps=  extra34 Non-Protein energy; two coupling groups -
more accurate
tau_t= 0.10.1 0.1; time constant, in ps
ref_t=  310310 310 ; reference temperature, one for each
group, in K
;

Energy contain the residues that i needed
extra34 contain all the remaining ligand and receptor atom
non-protein contain sol and ion.

I got the energy file after mdrun -rerun

I used the g_energy term

It give me the following output
End your selection with an empty line or a zero.
---
  1  G96Angle 2  Proper-Dih.  3  Improper-Dih.4
LJ-14
  5  Coulomb-14   6  LJ-(SR)  7  LJ-(LR)  8
Disper.-corr.
  9  Coulomb-(SR)10  Coul.-recip.11  Potential   12
Kinetic-En.
 13  Total-Energy14  Temperature 15  Pres.-DC16
Pressure
 17  Constr.-rmsd18  Box-X   19  Box-Y   20
Box-Z
 21  Volume  22  Density 23  pV  24
Enthalpy
 25  Vir-XX  26  Vir-XY  27  Vir-XZ  28
Vir-YX
 29  Vir-YY  30  Vir-YZ  31  Vir-ZX  32
Vir-ZY
 33  Vir-ZZ  34  Pres-XX 35  Pres-XY 36
Pres-XZ
 37  Pres-YX 38  Pres-YY 39  Pres-YZ 40
Pres-ZX
 41  Pres-ZY 42  Pres-ZZ 43  #Surf*SurfTen   44
Box-Vel-XX
 45  Box-Vel-YY  46  Box-Vel-ZZ  47  Mu-X48
Mu-Y
 49  Mu-Z50  T-extra34   51  T-non-Protein   52
T-energy
 53  Lamb-extra3454
Lamb-non-Protein
 55  Lamb-energy


So I confused. though it shows the energy group, which option should i have
to choose ??

What is Lamb-energy???

Is I did any mistake??? or I have to use any else command ??

Thank you in advance

With best wishes and regards.
Rama david.






On Fri, Oct 5, 2012 at 7:54 PM, Justin Lemkul jalem...@vt.edu wrote:



 On 10/5/12 10:16 AM, rama david wrote:

 Hi gromacs friends,

 I completed the simulation of receptor and ligand,
 I visualized the trajectory in the vmd I found  most of the time C
 terminal
 (ARG) interact with receptor ( 320 ASP) .
 I want to find out these interaction energy between these two residues in
 the simulation.



 How to find  these interaction energy

 ( include the LJ and electrostatic interaction)..


 I explained how to do this already.  You need properly set energygrps in
 the .mdp file and an index file that specifies those groups.  The
 quantities you want will then be in the .edr file like all other energy
 terms.

 -Justin

 --
 ==**==

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

 ==**==
 --
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Re: [gmx-users] Interaction energy..

Hi justin,
Ok now I get
I have to modify mdp parameter ..

Thank you,
With best wishes and regards,
Rama david

On Fri, Oct 5, 2012 at 9:47 PM, Justin Lemkul jalem...@vt.edu wrote:



 On 10/5/12 11:46 AM, rama david wrote:

 Thank you for your Help.

 I did the following tc-groups

 tcoupl= V-rescale; modified Berendsen thermostat
 tc-grps=  extra34 Non-Protein energy; two coupling groups -
 more accurate
 tau_t= 0.10.1 0.1; time constant, in ps
 ref_t=  310310 310 ; reference temperature, one for each
 group, in K
 ;

 Energy contain the residues that i needed
 extra34 contain all the remaining ligand and receptor atom
 non-protein contain sol and ion.

 I got the energy file after mdrun -rerun

 I used the g_energy term

 It give me the following output
 End your selection with an empty line or a zero.
 --**--**---
1  G96Angle 2  Proper-Dih.  3  Improper-Dih.4
 LJ-14
5  Coulomb-14   6  LJ-(SR)  7  LJ-(LR)  8
 Disper.-corr.
9  Coulomb-(SR)10  Coul.-recip.11  Potential   12
 Kinetic-En.
   13  Total-Energy14  Temperature 15  Pres.-DC16
 Pressure
   17  Constr.-rmsd18  Box-X   19  Box-Y   20
 Box-Z
   21  Volume  22  Density 23  pV  24
 Enthalpy
   25  Vir-XX  26  Vir-XY  27  Vir-XZ  28
 Vir-YX
   29  Vir-YY  30  Vir-YZ  31  Vir-ZX  32
 Vir-ZY
   33  Vir-ZZ  34  Pres-XX 35  Pres-XY 36
 Pres-XZ
   37  Pres-YX 38  Pres-YY 39  Pres-YZ 40
 Pres-ZX
   41  Pres-ZY 42  Pres-ZZ 43  #Surf*SurfTen   44
 Box-Vel-XX
   45  Box-Vel-YY  46  Box-Vel-ZZ  47  Mu-X48
 Mu-Y
   49  Mu-Z50  T-extra34   51  T-non-Protein   52
 T-energy
   53  Lamb-extra3454
 Lamb-non-Protein
   55  Lamb-energy


 So I confused. though it shows the energy group, which option should i
 have
 to choose ??

 What is Lamb-energy???


 It is related to temperature coupling.


  Is I did any mistake??? or I have to use any else command ??


 I have told you to use energygrps (which is described in the manual) and
 you're specifying tc-grps.  Temperature coupling and energy calculation
 groups are very different concepts.


 -Justin

 --
 ==**==

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

 ==**==
 --
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Re: [gmx-users] Interaction energy..