Re: [gmx-users] (no subject)

[Rakesh Mishra]

Thanks Justin

I followed your suggestion. now I am able to restrain (immobile) any
molecule during pulling.

thanks for your help.

On Tue, Jan 2, 2018 at 4:56 PM, Rakesh Mishra  wrote:

> Dear all
>
> I am just a beginner in gromacs. I have installed gromacs 5.1 version.  I
> am doing  pulling for si-rna  (double stranded, 22 nucleotides each ). I
> am applying
> pulling code of  umbrella sampling. Using that, we have chosen 22nd number
> residue of chain A is under pulling with constant velocity rate in +ve x
> direction.  and residue 44 of  apposite chain B at the apposite end is
> taking as reference . Now I am thinking to make the reference residue 44 as
> immobile. But when
> after simulation I am trying to see the trajectory . Then I Am finding that
> the residue n 44 (reference residue of pulling) is also moving and which is
> in apposite direction.
> even it is showing that reference residue 44 is crossing the box wall in
> -ve x direction.
>
> My aim is to pull residue n 22 of chain-A of si-rna by making reference
> residue n 44 of chain-B of si-rnA as a immobile, i mean no need for big
> motion in apposite direction.
>
> --
> * Rakesh Kumar Mishra*
> *  (RA)CSD  SINP Kolkata, India*
>
> *E-mail - rakesh.mis...@saha.ac.in  *
>
> *Phone n. +91 9473662491 <094736%2062491>, +91877749632*
>



-- 
* Rakesh Kumar Mishra*
*  (RA)CSD  SINP Kolkata, India*

*E-mail - rakesh.mis...@saha.ac.in  *

*Phone n. +91 9473662491, +91877749632*
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] KALP in DPPC

[kordzadeh]

Hi Dr.Lemkul

Thank you very much for your answer

I will select 310 kelvin becauase I want to investigate physiological condition.

in tutorial weve used semiisotropic pressure coupling and normal and 
lateral pressure are determined 1 bar. 

why? is it related to surface tension?

if we want to surface tension be zero, should we set lateral pressure zero?

Thank you very much for your help

Regards

Azadeh

-- 
This email was Anti Virus checked by  Security Gateway.
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] atom types consistency between atb and charmm

[MD]

Will do :)
Ming

On Thu, Jan 4, 2018 at 6:06 PM, Justin Lemkul  wrote:

>
>
> On 1/4/18 12:20 PM, MD wrote:
>
>> Hi Justin,
>>
>> Then what would be the solution if I need to add a modified amino acid in
>> merged.rtp and ffbonded.itp I wonder? My amino acid will have a fairly
>> large ligand covalently bonded with.
>>
>
> I've expounded upon CHARMM parametrization tools and methodology many
> times on this mailing list. Please search the archive to avoid me having to
> type out a long thesis that I've already posted many times before :)
>
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] KALP in DPPC

[Justin Lemkul]

On 1/4/18 2:15 PM, kordza...@aut.ac.ir wrote:
  


Hi all

in tutorial KALP in DPPC, why we set temperature above the phase transittion 
temperature whereas physiological temperature is 310 kelvin.


It depends on what you want to model; in the illustrated case we want a 
liquid crystalline state, not a gel phase.



I want too investigate interaction of carbon nano tube and DPPC bilayer and I 
think , I should set temperature to 310.

is that right?


Again it depends on what you want to model. At 310 K, the DPPC will 
become a gel phase. If that's what you want, then go ahead. If it's not, 
you'll need to decide the best approach based on the phase transition 
temperature and how well the given force field models the phase transition.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] atom types consistency between atb and charmm

[Justin Lemkul]

On 1/4/18 12:20 PM, MD wrote:

Hi Justin,

Then what would be the solution if I need to add a modified amino acid in
merged.rtp and ffbonded.itp I wonder? My amino acid will have a fairly
large ligand covalently bonded with.


I've expounded upon CHARMM parametrization tools and methodology many 
times on this mailing list. Please search the archive to avoid me having 
to type out a long thesis that I've already posted many times before :)


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Minimization changes system box shape after using ParmEd

[Justin Lemkul]

On 1/4/18 5:42 PM, Crystal Vander Zanden wrote:

Hello GROMACS community,

I am having problems maintaining the shape of my system box after using
ParmEd to convert from Amber to Gromacs format.

I parameterized a system with AmberTools (peptide solvated in an octahedral
box).  I then converted the Amber files (.inpcrd and .prmtop) to GROMACS
format (.gro and .top) using ParmEd.  I used VMD to look at the system, and
it looks ok (peptide still centered in an octahedral box). (
http://i1380.photobucket.com/albums/ah185/cmvander/parmed_zpssaq6ldnb.png)

Next I did an energy minimization in GROMACS.  VMD displayed the resulting
.gro file as a triclinic box and the peptide is no longer centered. (
http://i1380.photobucket.com/albums/ah185/cmvander/minimized_zpsekznpl3w.png
)

I think that the system really is still an octahedral box because I can see
the octahedral box boundaries within the triclinic box. I overlaid both
systems and the protein is in the same spot (
http://i1380.photobucket.com/albums/ah185/cmvander/image_overlay_zpsepfpqkvl.png).
Also I got reasonable minimization energies.

Steepest Descents converged to Fmax < 1000 in 337 steps
Potential Energy  = -3.1393012e+05
Maximum force =  9.0675385e+02 on atom 363
Norm of force =  3.5674736e+01

Am I just doing something wrong to cause VMD to display my system
incorrectly, or is there a more serious issue?  Either way, I’d be happy to
know how to fix it!


GROMACS always uses a triclinic representation by default. Convert it to 
the desired shape with trjconv:


gmx trjconv -pbc mol -ur compact

-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] Minimization changes system box shape after using ParmEd

[Crystal Vander Zanden]

Hello GROMACS community,

I am having problems maintaining the shape of my system box after using
ParmEd to convert from Amber to Gromacs format.

I parameterized a system with AmberTools (peptide solvated in an octahedral
box).  I then converted the Amber files (.inpcrd and .prmtop) to GROMACS
format (.gro and .top) using ParmEd.  I used VMD to look at the system, and
it looks ok (peptide still centered in an octahedral box). (
http://i1380.photobucket.com/albums/ah185/cmvander/parmed_zpssaq6ldnb.png)

Next I did an energy minimization in GROMACS.  VMD displayed the resulting
.gro file as a triclinic box and the peptide is no longer centered. (
http://i1380.photobucket.com/albums/ah185/cmvander/minimized_zpsekznpl3w.png
)

I think that the system really is still an octahedral box because I can see
the octahedral box boundaries within the triclinic box. I overlaid both
systems and the protein is in the same spot (
http://i1380.photobucket.com/albums/ah185/cmvander/image_overlay_zpsepfpqkvl.png).
Also I got reasonable minimization energies.

Steepest Descents converged to Fmax < 1000 in 337 steps
Potential Energy  = -3.1393012e+05
Maximum force =  9.0675385e+02 on atom 363
Norm of force =  3.5674736e+01

Am I just doing something wrong to cause VMD to display my system
incorrectly, or is there a more serious issue?  Either way, I’d be happy to
know how to fix it!

Thanks in advance for any advice!  I really appreciate it!
Crystal

Some extra information---
The last line of the AMBER .inpcrd file:
68.4778914  68.4778914  68.4778914 109.4712190 109.4712190 109.4712190

The last line of the .gro file from ParmEd conversion:
6.84779   6.45616   5.59120   0.0   0.0  -2.28260   0.0
-2.28260  -3.22808

The last line of the em.gro file resulting from energy minimization:
6.84779   6.45616   5.59120   0.0   0.0  -2.28260   0.0
-2.28260  -3.22808

I tried using editconf as suggested here (
http://manual.gromacs.org/programs/gmx-editconf.html), but I don’t think
this is the right track for my problem. Minimization failed when I tried to
use the structure I made by doing this.
“To convert a truncated octrahedron file produced by a package which uses a
cubic box with the corners cut off (such as GROMOS), use:
*>>>*gmx editconf -f in -rotate 0 45 35.264 -bt o -box veclen -o out
where veclen is the size of the cubic box times sqrt(3)/2.”


-- 
Crystal M. Vander Zanden, Ph.D.
ASERT Postdoctoral Fellow (IRACDA)
University of New Mexico, Albuquerque
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] Possible issues from a precision mismatch.

[Diego Alberto Muñoz Gacitua]

Greeting gromacs users,

 I've been running some simulations on a local computer running Gromacs
2016.4 compiled with single precision. Recently we've been given access to
HPC resources, but this HPC has the same version of Gromacs installed with
double presicion.

 Are there any issues when continuing a single precision simulation on a
double precision compiled Gromacs? Or should I request a single precision
compilation to be installed in this HPC?

Regards.


-- 
Diego Muñoz G.
Departamento de Química
Laboratorio Fisicoquímica Molecular
Facultad de Ciencias
Universidad de Chile
Tel: 56 9 5137 2029
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] KALP in DPPC

[kordzadeh]

 

Hi all

in tutorial KALP in DPPC, why we set temperature above the phase transittion 
temperature whereas physiological temperature is 310 kelvin.

I want too investigate interaction of carbon nano tube and DPPC bilayer and I 
think , I should set temperature to 310.

is that right?

Thank you very much

Regards

Azadeh

 

-- 
This email was Anti Virus checked by  Security Gateway.
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] atom types consistency between atb and charmm

[MD]

Hi Justin,

Then what would be the solution if I need to add a modified amino acid in
merged.rtp and ffbonded.itp I wonder? My amino acid will have a fairly
large ligand covalently bonded with.

Ming

On Thu, Jan 4, 2018 at 8:43 AM, Justin Lemkul  wrote:

>
>
> On 1/4/18 8:41 AM, MD wrote:
>
>> Hi Gromacs folks,
>>
>> I was using atb to generate topology files for my ligands and modified
>> amino acid and needed to change the atom types from atb output to make
>> them
>> consistent with charmm, the force field I used, since I need to include a
>> modified amino acid.
>>
>> I wonder if there is a way to change all the atom types systematically and
>> automatically or it is the only way to change them manually?
>>
>
> You can't combine anything from ATB (which is for the united-atom GROMOS
> force field) with CHARMM. Mixing and matching force fields is fundamentally
> invalid because they all rely on different assumptions, functional forms,
> etc.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] umbrella sampling, LINCS WARNING

[Justin Lemkul]

On 1/4/18 2:48 AM, rose rahmani wrote:

Hello;

I'm doing umbrella sampling, protein is getting closer to ZnS, but i get
some step files and run crashed just 107sec to end. Would it be because of
protein got very close to ZnS? Would you please help me?


A COM distance of 0.3 nm is going to place atoms well within the steep 
LJ repulsive regime, so naturally forces are going to build up. Watch 
the trajectory and see what's happening.


-Justin


With regards


-
this is pullf.xvg

0.  -0.000579208
0.0020  2.45011
0.0040  4.89696
0.0060  7.35804
0.0080  9.82449
0.0100  12.2863
0.0120  14.7352
0.0140  17.1628
0.0160  19.5634

.
.
.
1956.0480   -100532
1956.0500   -100532
1956.0520   -100531
1956.0540   -100530
1956.0560   -100529
1956.0580   -100528
1956.0600   -100527
1956.0620   -100526
---
this is pullx.xvg

0.  4.287   1.73577
0.1000  4.287   1.72023
0.2000  4.287   1.73131
0.3000  4.287   1.75326
0.4000  4.287   1.77348
0.5000  4.287   1.76939
0.6000  4.287   1.75636
0.7000  4.287   1.73677
0.8000  4.287   1.71755
0.9000  4.287   1.70901
1.  4.287   1.72336

.
.
.

1953.2000   4.287   0.324765
1953.3000   4.287   0.323972
1953.4000   4.287   0.326929
1953.5000   4.287   0.323881
1953.6000   4.287   0.323358
1953.7000   4.287   0.325145
1953.8000   4.287   0.32516
1953.9000   4.287   0.324791
1954.   4.287   0.325144
1954.1000   4.287   0.324902
1954.2000   4.287   0.324985
1954.3000   4.287   0.324877
1954.4000   4.287   0.323429
1954.5000   4.287   0.32637
1954.6000   4.287   0.324941
1954.7000   4.

---
this is md_pull.mdp;

integrator   = md
dt   = 0.002
nsteps   = 100
nstxout  = 5000
nstvout  = 5000
nstfout  = 500
nstlog   = 500
nstenergy= 1000
nstxtcout= 1000
nstlist  = 10
rlist= 1.5
coulombtype  = pme
rcoulomb = 1.5
vdwtype  = Switch
rvdw_switch  = 1.0
rvdw = 1.2
pcoupl   = no
gen_vel  = no
constraints  = h-bonds
ns_type  = grid
pbc  = xy
freezegrps   = WAL ZnS
freezedim= Y Y Y Y Y Y
energygrp-excl   = WAL WAL ZnS ZnS
energygrps   = SOL WAL ZnS Protein NA CL
nwall= 2
wall-atomtype= C C
wall-type= 9-3
wall-density = 150 150
wall-ewald-zfac  = 3
ewald-geometry   = 3dc
fourierspacing   = 0.12
tcoupl   = v-rescale
tc-grps  = System
tau-t= 0.1
ref-t= 300

; Pull code
pull= umbrella
pull_ngroups= 1
pull_group0 = ZnS
pull_group1 = Protein
pull_geometry   = direction
pull_vec1   = 0 0 1
pull_dim= N N Y
pull_rate1  = -0.011; 1 nm per  ns
pull_k1 = 5000
pull_start  = yes
pull_nstxout= 50

--
This is pull.job


Step 978195, time 1956.39 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.04, max 0.10 (between atoms 782 and 780)
bonds that rotated more than 30 degrees:
  atom 1 atom 2  angle  previous, current, constraint length
 770769   61.40.1090   0.1090  0.1090
 779778   42.00.1010   0.1010  0.1010

Step 978197, time 1956.39 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.429802, max 1.468930 (between atoms 783 and 780)
bonds that rotated more than 30 degrees:
  atom 1 atom 2  angle  previous, current, constraint length
 773771   90.00.1112   0.1202  0.1090
 770769   32.80.1090   0.1090  0.1090
 779778   90.00.1010   0.1232  0.1010
 783780   90.00.1090   0.2691  0.1090
Wrote pdb files with previous and current coordinates

Step 978198, time 1956.4 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 2.212948, max 5.521000 (between atoms 773 and 771)
bonds that rotated more than 30 degrees:
  atom 1 atom 2  angle  previous, current, constraint length
 773771   90.00.1202   0.7108  0.1090
 772771   47.80.1105   0.1031  0.1090
 770769   90.00.1090   0.1142  0.1090
 779778   90.00.1232   0.6381  0.1010
 783780   57.80.2691   0.1086  0.1090
Wrote pdb files with previous and current coordinates

Step 978199, time 1956.4 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.451943, max 1.210712 (between atoms 770 and 769)
bonds that rotated more than 30 degrees:
  atom 1 atom 2  angle  

Re: [gmx-users] atom types consistency between atb and charmm

[Justin Lemkul]

On 1/4/18 8:41 AM, MD wrote:

Hi Gromacs folks,

I was using atb to generate topology files for my ligands and modified
amino acid and needed to change the atom types from atb output to make them
consistent with charmm, the force field I used, since I need to include a
modified amino acid.

I wonder if there is a way to change all the atom types systematically and
automatically or it is the only way to change them manually?


You can't combine anything from ATB (which is for the united-atom GROMOS 
force field) with CHARMM. Mixing and matching force fields is 
fundamentally invalid because they all rely on different assumptions, 
functional forms, etc.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] atom types consistency between atb and charmm

[MD]

Hi Gromacs folks,

I was using atb to generate topology files for my ligands and modified
amino acid and needed to change the atom types from atb output to make them
consistent with charmm, the force field I used, since I need to include a
modified amino acid.

I wonder if there is a way to change all the atom types systematically and
automatically or it is the only way to change them manually?

Thank you,

Ming
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Related to REMD

[ISHRAT JAHAN]

Thank you Sudip


On Thu, Jan 4, 2018 at 2:50 PM, Sudip Das  wrote:

> Hi Ishrat,
>
> As per REMD, you are supposed to generate different .tpr files for
> different replicas at their corresponding temperature and simulate
> simultaneously all the replicas. As for example, if you are having 5
> replicas,
>
> replica:  0   1 234
> temp:300305312322335
>
> Have a look into GROMACS REMD tutorial.
>
> Regards,
> Sudip
>
> ‌
>
> Sudip Das
>
> PhD Student
> C/o. Prof. S. Balasubramanian
> Molecular Simulations Lab
> Chemistry and Physics of Materials Unit (CPMU)
> Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR)
> Bangalore, India
>
> On Thu, Jan 4, 2018 at 12:20 PM, ISHRAT JAHAN  wrote:
>
> > Hi Sudip
> > For doing REMD,I have generated the five seed conformation using trjconv
> > command. I have taken only 10 temperature from the temperature generating
> > tool, now i want to know whether i have to generate different .tpr file
> > using one conformation at all temperature or all conformations at all
> > temperature. Will you please tell me what to do as i am unable to
> > understand?
> > Thanks in advance
> >
> >
> > On Tue, Jan 2, 2018 at 4:55 PM, Sudip Das  wrote:
> >
> > > Hi Ishrat,
> > >
> > >
> > > On Tue, Jan 2, 2018 at 4:14 PM, ISHRAT JAHAN 
> > wrote:
> > >
> > > > Dear all,
> > > > I am trying to do REMD simulation. I had equillbrated the system for
> > 5ns
> > > > and extracted the seed conformation at 3ns using the command-
> > > > gmx trjconv -f traj.trr -o 3ns.gro -s topol.tpr -dump 3000 -pbc mol
> > > > I had used temperature generator for REMD simulation from
> > > > folding.bmc.uu.se/remd with transition probability of 0.25 in
> > > temperature
> > > > range of 290-400K.it gives too many replica and i want only 10
> replica.
> > >
> > > will anyone tell me what criteria should be taken for taking 10
> replicas
> > > >
> > >
> > > It seems that your system size is reasonably large. You can try using
> > > replica exchange with solute scaling (REST2 method) which is basically
> > > comes under Hamiltonian replica exchange. It will reduce the number of
> > > replicas by scaling the potential energy surface with respect to
> > effective
> > > temperature of the corresponding replica.
> > >
> > >
> > > > and also tell how to extract the one seed conformation from multiple
> > seed
> > > > conformation which i had generated using above command.
> > > >
> > >
> > > See the several options under the module trjconv by typing the command:
> > > gmx trjconv -h
> > >
> > >
> > > Regards,
> > > Sudip
> > >
> > >
> > > Thanks in advance
> > > > --
> > > > Gromacs Users mailing list
> > > >
> > > > * Please search the archive at http://www.gromacs.org/
> > > > Support/Mailing_Lists/GMX-Users_List before posting!
> > > >
> > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > >
> > > > * For (un)subscribe requests visit
> > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> > > > send a mail to gmx-users-requ...@gromacs.org.
> > > >
> > >
> > > ‌
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at http://www.gromacs.org/
> > > Support/Mailing_Lists/GMX-Users_List before posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-requ...@gromacs.org.
> > >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at http://www.gromacs.org/
> > Support/Mailing_Lists/GMX-Users_List before posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Related to REMD

[Sudip Das]

Hi Ishrat,

As per REMD, you are supposed to generate different .tpr files for
different replicas at their corresponding temperature and simulate
simultaneously all the replicas. As for example, if you are having 5
replicas,

replica:  0   1 234
temp:300305312322335

Have a look into GROMACS REMD tutorial.

Regards,
Sudip

‌

Sudip Das

PhD Student
C/o. Prof. S. Balasubramanian
Molecular Simulations Lab
Chemistry and Physics of Materials Unit (CPMU)
Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR)
Bangalore, India

On Thu, Jan 4, 2018 at 12:20 PM, ISHRAT JAHAN  wrote:

> Hi Sudip
> For doing REMD,I have generated the five seed conformation using trjconv
> command. I have taken only 10 temperature from the temperature generating
> tool, now i want to know whether i have to generate different .tpr file
> using one conformation at all temperature or all conformations at all
> temperature. Will you please tell me what to do as i am unable to
> understand?
> Thanks in advance
>
>
> On Tue, Jan 2, 2018 at 4:55 PM, Sudip Das  wrote:
>
> > Hi Ishrat,
> >
> >
> > On Tue, Jan 2, 2018 at 4:14 PM, ISHRAT JAHAN 
> wrote:
> >
> > > Dear all,
> > > I am trying to do REMD simulation. I had equillbrated the system for
> 5ns
> > > and extracted the seed conformation at 3ns using the command-
> > > gmx trjconv -f traj.trr -o 3ns.gro -s topol.tpr -dump 3000 -pbc mol
> > > I had used temperature generator for REMD simulation from
> > > folding.bmc.uu.se/remd with transition probability of 0.25 in
> > temperature
> > > range of 290-400K.it gives too many replica and i want only 10 replica.
> >
> > will anyone tell me what criteria should be taken for taking 10 replicas
> > >
> >
> > It seems that your system size is reasonably large. You can try using
> > replica exchange with solute scaling (REST2 method) which is basically
> > comes under Hamiltonian replica exchange. It will reduce the number of
> > replicas by scaling the potential energy surface with respect to
> effective
> > temperature of the corresponding replica.
> >
> >
> > > and also tell how to extract the one seed conformation from multiple
> seed
> > > conformation which i had generated using above command.
> > >
> >
> > See the several options under the module trjconv by typing the command:
> > gmx trjconv -h
> >
> >
> > Regards,
> > Sudip
> >
> >
> > Thanks in advance
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at http://www.gromacs.org/
> > > Support/Mailing_Lists/GMX-Users_List before posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-requ...@gromacs.org.
> > >
> >
> > ‌
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at http://www.gromacs.org/
> > Support/Mailing_Lists/GMX-Users_List before posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Defining single, double and triple bonds

[Mark Abraham]

Hi,

You can define bonds of different strengths, but the connectivity and
spatial arrangement are not expressed in the way you suggest.

Mark

On Thu, Jan 4, 2018 at 5:27 AM SUVANKAR GHOSH 
wrote:

>
> Hi, Is there any option to define single, double and triple bonds in my
> topology.
>
> --
> Suvankar Ghosh
> Research Scholar,
> Computational Structural Biology Lab,
> Dept. of Biosciences and Bioengineering (BSBE),
> Indian Institute of Technology Guwahati (IITG)
> Guwahati 781039, Assam, India
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] warning:Long Bond

[Mark Abraham]

Hi,

On Wed, Jan 3, 2018 at 10:26 PM Saleheh Heidari 
wrote:

> Hi Justin
>
> Thanks for your reply. As you said I checked the atom numbers which gave
> the long bond warning, and there was no problem with the intra-residual
> bonds in all the residues, but the warning was given for the inter-residual
> bonds, i.e. the bond between the last atom of a residue and the first atom
> of the next residue.


So why are they so long?


> I also checked the pdb file by visualizing it with VMD
> and it looked correct.


Unfortunately not relevant. VMD guesses where bonds are located based on
its own heuristics, and such long bonds will lead to nothing being shown.

Should I continue and ignore the warnings assuming
> that the structure returns to the proper conformation after minimization?
>

You can try, but it'll probably explode immediately.

Mark


> I would greatly appreciate your help.
>
> Regards,
>
> Saleheh Heydari
>
>
>
> On Fri, Dec 22, 2017 at 3:22 AM, Justin Lemkul  wrote:
>
> >
> >
> > On 12/21/17 12:09 PM, Saleheh Heidari wrote:
> >
> >> Dear Gromacs Users
> >>
> >> I am trying to run a molecular dynamics simulation with a DNA
> tetrahedron.
> >> I am using Gromacs-2016.4 having the forcefield AMBER99SB-ILDN.
> >>
> >> The topology file has been successfully generated.
> >>
> >> However I am concerned with the following comment in the output of
> >> pdb2gmx,
> >> these are the gromacs output for the first chain:
> >>
> >> 
> >> There are 4 chains and 0 blocks of water and 220 residues with 4497
> atoms
> >>
> >>chain  #res #atoms
> >>1 'A'55   1119
> >>2 'B'55   1133
> >>3 'C'55   1123
> >>4 'D'55   1122
> >>
> >> All occupancies are one
> >> Opening force field file
> >> /usr/local/bin/gromacs/share/gromacs/top/amber99sb-ildn.ff/atomtypes.atp
> >> Atomtype 67
> >> Reading residue database... (amber99sb-ildn)
> >> Opening force field file
> >>
> /usr/local/bin/gromacs/share/gromacs/top/amber99sb-ildn.ff/aminoacids.rtp
> >> Residue 93
> >> Sorting it all out...
> >> Opening force field file
> >> /usr/local/bin/gromacs/share/gromacs/top/amber99sb-ildn.ff/dna.rtp
> >> Residue 109
> >> Sorting it all out...
> >> Opening force field file
> >> /usr/local/bin/gromacs/share/gromacs/top/amber99sb-ildn.ff/rna.rtp
> >> Residue 125
> >> Sorting it all out...
> >> Opening force field file
> >>
> /usr/local/bin/gromacs/share/gromacs/top/amber99sb-ildn.ff/aminoacids.hdb
> >> Opening force field file
> >> /usr/local/bin/gromacs/share/gromacs/top/amber99sb-ildn.ff/dna.hdb
> >> Opening force field file
> >> /usr/local/bin/gromacs/share/gromacs/top/amber99sb-ildn.ff/rna.hdb
> >> Opening force field file
> >> /usr/local/bin/gromacs/share/gromacs/top/amber99sb-ildn.ff/a
> >> minoacids.n.tdb
> >> Opening force field file
> >> /usr/local/bin/gromacs/share/gromacs/top/amber99sb-ildn.ff/a
> >> minoacids.c.tdb
> >> Processing chain 1 'A' (1119 atoms, 55 residues)
> >> Identified residue DT51 as a starting terminus.
> >> Identified residue DT355 as a ending terminus.
> >> 8 out of 8 lines of specbond.dat converted successfully
> >> Opening force field file
> >>
> /usr/local/bin/gromacs/share/gromacs/top/amber99sb-ildn.ff/aminoacids.arn
> >> Opening force field file
> >> /usr/local/bin/gromacs/share/gromacs/top/amber99sb-ildn.ff/dna.arn
> >> Opening force field file
> >> /usr/local/bin/gromacs/share/gromacs/top/amber99sb-ildn.ff/rna.arn
> >> Checking for duplicate atoms
> >> Generating any missing hydrogen atoms and/or adding termini.
> >> Now there are 55 residues with 1747 atoms
> >> Chain time...
> >> Making bonds...
> >> Warning: Long Bond (30-31 = 0.277244 nm)
> >> Warning: Long Bond (62-63 = 0.306978 nm)
> >> Warning: Long Bond (92-93 = 0.350789 nm)
> >> Warning: Long Bond (124-125 = 0.320527 nm)
> >> Warning: Long Bond (157-158 = 0.340453 nm)
> >> Warning: Long Bond (189-190 = 0.273576 nm)
> >> Warning: Long Bond (219-220 = 0.268338 nm)
> >> Warning: Long Bond (251-252 = 0.277104 nm)
> >> Warning: Long Bond (283-284 = 0.360828 nm)
> >> Warning: Long Bond (315-316 = 0.320431 nm)
> >> Warning: Long Bond (348-349 = 0.329925 nm)
> >> Warning: Long Bond (381-382 = 0.334705 nm)
> >> Warning: Long Bond (413-414 = 0.330311 nm)
> >> Warning: Long Bond (477-478 = 0.354473 nm)
> >> Warning: Long Bond (510-511 = 0.254489 nm)
> >> Warning: Long Bond (542-543 = 0.659257 nm)
> >> Warning: Long Bond (574-575 = 0.331438 nm)
> >> Warning: Long Bond (606-607 = 0.757552 nm)
> >> Warning: Long Bond (638-639 = 0.277172 nm)
> >> Warning: Long Bond (670-671 = 0.307023 nm)
> >> Warning: Long Bond (700-701 = 0.296372 nm)
> >> Warning: Long Bond (730-731 = 0.296309 nm)
> >> Warning: Long Bond (760-761 = 0.350757 nm)
> >> Warning: Long Bond (792-793 = 0.273076 nm)
> >> Warning: Long Bond (822-823 = 0.344508 nm)
> >> Warning: Long Bond (855-856 = 0.25441 nm)
> >> Warning: Long Bond (887-888 = 0.360906 nm)
> >> Warning: Long Bond (919-920 = 0.320435 nm)
>