[gmx-users] (no subject)

[Upasana Ray]

Dear  user,

 I have generated my final protein.pdb file by using trjconv command from
.xtc file. The size of my pdb file is 0.98 GB, so whenever I am opening it
for docking purpose my computer is freezing. Now how can I reduce my pdb
file size  from GB to MB for using it properly. please help me to deal
 with this problem.
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[gmx-users] warning 1-4 interaction in QMMM simulation

[andrian]

Dear gromacs users

i was trying to perform micro-iterative QMMM optimization using 
gromacs/orca interface... in mdp file, i set bOpt = yes, then i got a 
warning like this:


"Warning: 1-4 interaction between 3 and 6 at distance 3.565 which is 
larger than the 1-4 table size 2.000 nm, These are ignored for the rest 
of the simulation, This usually means your system is exploding, if not, 
you should increase table-extension in your mdp file, or with user 
tables increase the table size"


note: my sistem has been successfully minimized and also NVT restrained 
simulation...



anyone can help ? thank you so much..

cheers

***
title= my_mdp_file
cpp  = /lib/cpp
include  =
define   =

integrator   = steep

tinit= 0
dt   = 0.01
nsteps   = 100

nstcomm  = 1
comm_grps= system

emtol= 100.0
emstep   = 0.001

nstxout  = 1
nstvout  = 1
nstfout  = 1
nstlog   = 1
nstenergy= 1
nstxtcout= 1
xtc-precision= 1000
xtc_grps = system
energy_grps  = QMatoms MMatoms

nstlist  = 1
ns_type  = grid
pbc  = xyz
rlist= 1.0
coulombtype  = PME
rcoulomb-switch  = 0
rcoulomb = 1.0
epsilon_r= 1.0
fourierspacing  = 0.12
ewald_rtol = 1e-5

vdwtype  = Cut-off
rvdw = 1.0
DispCorr = No

QMMM = yes
QMMM-grps= QMatoms
QMmethod = RHF
QMbasis  = STO-3G
QMMMscheme   = normal
QMcharge = 1
QMmult   = 1
bOPT = yes
bTS  = no

constraints  = none


! AM1 PModel

%scf
  SCFMode Direct
  MaxIter 1500
  UseCheapInts true
end

qmmm.inp file produced by gromacs

#input-file generated by gromacs
!QMMMOpt TightSCF
! AM1 PModel


%scf
  SCFMode Direct
  MaxIter 1500
  UseCheapInts true
end
%geom
   Constraints
{C 0 C}
{C 8 C}
 end
   end
*xyz  1 1
  6 109.5018196  61.3748932  61.6309643
  1  2.3429996   2.3269998   2.5830004
  1  2.275   2.484   2.568
  6  2.4526897   2.4437210   2.4452071
  1  2.5284982   2.3686990   2.4200514
  8  2.5167450   2.5439975   2.5247785
  1  2.4429335   2.4939966   2.3479901
  1  2.4590001   2.579   2.5840002
  1 12.1445608  12.8626895  13.1234348
  8  2.7731431   2.5095880   2.3919705
  1  2.8239998   2.581   2.4270001
  1  2.696   2.5050002   2.464
  1  2.707   2.5490001   2.326
*

--
Andrian Saputra
Department of Pharmaceutical Science
Sumatera Institute of Technology, Indonesia

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Re: [gmx-users] md-vv integrator on gromacs 4.5.5

[Yao Li]

Thank you for your suggestion. I checked the release notes and saw the bug 
reported in gromacs 4.6.

Thanks again,
Yao


> 在 2016年5月13日，17:51，Justin Lemkul  写道：
> 
> 
> 
>> On 5/13/16 5:49 PM, LiYao wrote:
>> Hi gromacs users,
>> 
>> I tried to run md-vv along with nose-hoover thermostat on gromaces 4.5.5 but 
>> it resulted in a temperature 300 K higher than the reference temperature. 
>> However, I run the same simulation on gromacs 4.6.5 and it worked well. Has 
>> anyone encountered the same problem? Can I still incorporate nose-hoover 
>> with md-vv integrator on 4.5.5?
> 
> Probably a bug that has long since been fixed.  This is a hazard of trying to 
> use deprecated software :)  Upgrade and you should be fine.
> 
> -Justin
> 
> -- 
> ==
> 
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> 
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
> 
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
> 
> ==
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Re: [gmx-users] Restart simulation from checkpoint file with fewer nodes

[Husen R]

thanks a lot for your fast response.

I have tried it, and it failed. I ask in this forum just to make sure.
However, there was something in my cluster that probably make it failed.
I'll handle it first and then retry to restart again.

Regards,

Husen

On Sat, May 14, 2016 at 7:58 AM, Justin Lemkul  wrote:

>
>
> On 5/13/16 8:53 PM, Husen R wrote:
>
>> Dear all
>>
>> Does simulation able to be restarted from checkpoint file with fewer
>> nodes ?
>> let's say, at the first time, I run simulation with 3 nodes. At running
>> time, one of those nodes is crashed and the simulation is terminated.
>>
>> I want to restart that simulation immadiately based on checkpoint file
>> with
>> the remaining 2 nodes. does gromacs support such case ?
>> I need help.
>>
>
> Have you tried it?  It should work.  You will probably get a note about
> the continuation not being exact due to a change in the number of cores,
> but the run should proceed fine.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
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Re: [gmx-users] Restart simulation from checkpoint file with fewer nodes

[Justin Lemkul]

On 5/13/16 8:53 PM, Husen R wrote:

Dear all

Does simulation able to be restarted from checkpoint file with fewer nodes ?
let's say, at the first time, I run simulation with 3 nodes. At running
time, one of those nodes is crashed and the simulation is terminated.

I want to restart that simulation immadiately based on checkpoint file with
the remaining 2 nodes. does gromacs support such case ?
I need help.


Have you tried it?  It should work.  You will probably get a note about the 
continuation not being exact due to a change in the number of cores, but the run 
should proceed fine.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Restart simulation from checkpoint file with fewer nodes

[Husen R]

I use Gromacs-5.1.2 and SLURM-15.08.10 as a resource manager.

On Sat, May 14, 2016 at 7:53 AM, Husen R  wrote:

> Dear all
>
> Does simulation able to be restarted from checkpoint file with fewer nodes
> ?
> let's say, at the first time, I run simulation with 3 nodes. At running
> time, one of those nodes is crashed and the simulation is terminated.
>
> I want to restart that simulation immadiately based on checkpoint file
> with the remaining 2 nodes. does gromacs support such case ?
> I need help.
>
> Thank you in advance.
> Regards,
>
> Husen
>
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[gmx-users] Restart simulation from checkpoint file with fewer nodes

[Husen R]

Dear all

Does simulation able to be restarted from checkpoint file with fewer nodes ?
let's say, at the first time, I run simulation with 3 nodes. At running
time, one of those nodes is crashed and the simulation is terminated.

I want to restart that simulation immadiately based on checkpoint file with
the remaining 2 nodes. does gromacs support such case ?
I need help.

Thank you in advance.
Regards,

Husen
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Re: [gmx-users] md-vv integrator on gromacs 4.5.5

[Justin Lemkul]

On 5/13/16 5:49 PM, LiYao wrote:

Hi gromacs users,

I tried to run md-vv along with nose-hoover thermostat on gromaces 4.5.5 but it 
resulted in a temperature 300 K higher than the reference temperature. However, 
I run the same simulation on gromacs 4.6.5 and it worked well. Has anyone 
encountered the same problem? Can I still incorporate nose-hoover with md-vv 
integrator on 4.5.5?



Probably a bug that has long since been fixed.  This is a hazard of trying to 
use deprecated software :)  Upgrade and you should be fine.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] md-vv integrator on gromacs 4.5.5

[LiYao]

Hi gromacs users,

I tried to run md-vv along with nose-hoover thermostat on gromaces 4.5.5 but it 
resulted in a temperature 300 K higher than the reference temperature. However, 
I run the same simulation on gromacs 4.6.5 and it worked well. Has anyone 
encountered the same problem? Can I still incorporate nose-hoover with md-vv 
integrator on 4.5.5?

Thanks,
Yao
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Re: [gmx-users] LINCS WARNING Error in running production run in parallel of a MARTINI SYSTEM of membrane protein

[Tsjerk Wassenaar]

Hi Antara,

What commands did you use? At least make sure you add -rdd 1.6 to the
command line of mdrun, because the default value is too small for coarse
grain simulations.

Cheers,

Tsjerk

On Fri, May 13, 2016 at 8:12 PM, Antara mazumdar 
wrote:

> Dear users,
>
> I am trying to run a coarse grained simulation of a membrane protein in a
> mixed lipid billayer using martini model 2.2. I have already performed all
> the equilibration steps successfully on my desktop with GROMACS 5.1.0.
> However, when i try to execute its production run in parallel(having
> gromacs 5.1 version installed)  it complains of LINCS warning and
> terminates at step 0. But on the contrary, it runs on the desktop
> successfully. Kindly suggest something and please let me know if any more
> information is required from my side.
>
>
> Thanks!!
>
> Kind Regards,
> Antara
>
> --
> Junior research fellow(project)
> Systems biology group
> CSIR-Institute of Genomics & Integrative Biology
> South Campus
> New Delhi -  110020
> M : +91-9717970040
> --
>
>
>
> On Fri, May 13, 2016 at 11:11 PM, Antara mazumdar  >
> wrote:
>
> > Dear gromacs users,
> >
> > I am trying to run a coarse grained simulation of a membrane protein in a
> > mixed lipid billayer using martini model. I have already performed all
> the
> > equilibration steps successfully on my desktop. However, when i try to
> > execute its production run in parallel it complains of LINCS warning and
> > terminates at step 0. But on the contrary, it runs on the desktop
> > successfully. Kindly suggest something and please let me know if any more
> > information is required from my side.
> >
> >
> > Thanks!!
> >
> >
> >
> > Kind Regards,
> > Antara
> >
> > --
> > Junior research fellow(project)
> > Systems biology group
> > CSIR-Institute of Genomics & Integrative Biology
> > South Campus
> > New Delhi -  110020
> > M : +91-9717970040
> > --
> >
> >
> >
> --
> Gromacs Users mailing list
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> * Please search the archive at
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> posting!
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>



-- 
Tsjerk A. Wassenaar, Ph.D.
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Re: [gmx-users] LINCS WARNING Error in running production run in parallel of a MARTINI SYSTEM of membrane protein

[Antara mazumdar]

Dear users,

I am trying to run a coarse grained simulation of a membrane protein in a
mixed lipid billayer using martini model 2.2. I have already performed all
the equilibration steps successfully on my desktop with GROMACS 5.1.0.
However, when i try to execute its production run in parallel(having
gromacs 5.1 version installed)  it complains of LINCS warning and
terminates at step 0. But on the contrary, it runs on the desktop
successfully. Kindly suggest something and please let me know if any more
information is required from my side.


Thanks!!

Kind Regards,
Antara

--
Junior research fellow(project)
Systems biology group
CSIR-Institute of Genomics & Integrative Biology
South Campus
New Delhi -  110020
M : +91-9717970040
--



On Fri, May 13, 2016 at 11:11 PM, Antara mazumdar 
wrote:

> Dear gromacs users,
>
> I am trying to run a coarse grained simulation of a membrane protein in a
> mixed lipid billayer using martini model. I have already performed all the
> equilibration steps successfully on my desktop. However, when i try to
> execute its production run in parallel it complains of LINCS warning and
> terminates at step 0. But on the contrary, it runs on the desktop
> successfully. Kindly suggest something and please let me know if any more
> information is required from my side.
>
>
> Thanks!!
>
>
>
> Kind Regards,
> Antara
>
> --
> Junior research fellow(project)
> Systems biology group
> CSIR-Institute of Genomics & Integrative Biology
> South Campus
> New Delhi -  110020
> M : +91-9717970040
> --
>
>
>
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Re: [gmx-users] LINCS WARNING Error in running production run in parallel of a MARTINI SYSTEM of membrane protein

[Mark Abraham]

Hi,

Several things will make it easier to help - particularly your GROMACS
versions and how you ran mdrun. See also http://www.gromacs.org/Support

Mark

On Fri, May 13, 2016 at 7:42 PM Antara mazumdar 
wrote:

> Dear gromacs users,
>
> I am trying to run a coarse grained simulation of a membrane protein in a
> mixed lipid billayer using martini model. I have already performed all the
> equilibration steps successfully on my desktop. However, when i try to
> execute its production run in parallel it complains of LINCS warning and
> terminates at step 0. But on the contrary, it runs on the desktop
> successfully. Kindly suggest something and please let me know if any more
> information is required from my side.
>
>
> Thanks!!
>
>
>
> Kind Regards,
> Antara
>
> --
> Junior research fellow(project)
> Systems biology group
> CSIR-Institute of Genomics & Integrative Biology
> South Campus
> New Delhi -  110020
> M : +91-9717970040
> --
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
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>
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>
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[gmx-users] LINCS WARNING Error in running production run in parallel of a MARTINI SYSTEM of membrane protein

[Antara mazumdar]

Dear gromacs users,

I am trying to run a coarse grained simulation of a membrane protein in a
mixed lipid billayer using martini model. I have already performed all the
equilibration steps successfully on my desktop. However, when i try to
execute its production run in parallel it complains of LINCS warning and
terminates at step 0. But on the contrary, it runs on the desktop
successfully. Kindly suggest something and please let me know if any more
information is required from my side.


Thanks!!



Kind Regards,
Antara

--
Junior research fellow(project)
Systems biology group
CSIR-Institute of Genomics & Integrative Biology
South Campus
New Delhi -  110020
M : +91-9717970040
--
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Re: [gmx-users] pdb2gmx error after switching force fields

[Justin Lemkul]

On 5/13/16 11:04 AM, Irem Altan wrote:

Hi,

Thanks for the quick reply. Erasing the dihedral with CB worked. I’m actually 
using Gromacs 5.1.2.



Not sure how that's possible.  It should have been fixed prior to the release of 
5.1.1.


-Justin


Best,
Irem


On May 13, 2016, at 10:52 AM, Justin Lemkul  wrote:



On 5/13/16 10:49 AM, Irem Altan wrote:

Hi,

I have a .pdb file that I’ve used in simulations with amber99sb before. I have 
recently switched to amber03. When I do pdb2gmx, I get the following warning:

WARNING: WARNING: Residue 26 named GLY of a molecule in the input file was 
mapped
to an entry in the topology database, but the atom CB used in
an interaction of type dihedral in that entry is not found in the
input file. Perhaps your atom and/or residue naming needs to be
fixed.



There is an error in the AMBER03 .rtp file.  Either delete the dihedral that 
calls for CB or upgrade your GROMACS version.  I fixed this nearly two years 
ago, so you're using something really outdated :)


The same thing is repeated for a number of residues (26, 51, 59, 66, 67, 83, 
85, 95). The weird thing is, the residue numbers in the pdb file start from 
107, and gmx complains about lower numbers. Also, have I understood correctly 
that gmx complains that glycines in my input file don’t have beta carbons? What 
could be the problem here?



pdb2gmx uses its own internal numbering, starting from 1.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] pdb2gmx error after switching force fields

[Irem Altan]

Hi,

Thanks for the quick reply. Erasing the dihedral with CB worked. I’m actually 
using Gromacs 5.1.2.

Best,
Irem

> On May 13, 2016, at 10:52 AM, Justin Lemkul  wrote:
> 
> 
> 
> On 5/13/16 10:49 AM, Irem Altan wrote:
>> Hi,
>> 
>> I have a .pdb file that I’ve used in simulations with amber99sb before. I 
>> have recently switched to amber03. When I do pdb2gmx, I get the following 
>> warning:
>> 
>> WARNING: WARNING: Residue 26 named GLY of a molecule in the input file was 
>> mapped
>> to an entry in the topology database, but the atom CB used in
>> an interaction of type dihedral in that entry is not found in the
>> input file. Perhaps your atom and/or residue naming needs to be
>> fixed.
>> 
> 
> There is an error in the AMBER03 .rtp file.  Either delete the dihedral that 
> calls for CB or upgrade your GROMACS version.  I fixed this nearly two years 
> ago, so you're using something really outdated :)
> 
>> The same thing is repeated for a number of residues (26, 51, 59, 66, 67, 83, 
>> 85, 95). The weird thing is, the residue numbers in the pdb file start from 
>> 107, and gmx complains about lower numbers. Also, have I understood 
>> correctly that gmx complains that glycines in my input file don’t have beta 
>> carbons? What could be the problem here?
>> 
> 
> pdb2gmx uses its own internal numbering, starting from 1.
> 
> -Justin
> 
> -- 
> ==
> 
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> 
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
> 
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
> 
> ==
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Re: [gmx-users] Hydrophobic interaction analysis

[Justin Lemkul]

On 5/13/16 8:23 AM, Nikhil Maroli wrote:

We can analyse hydrogen bond numbers, what about total hydrogen bond
energy between two molecules over time like that in case of hydrophobic


There is no such energy term.  A hydrogen bond is largely electrostatic, though, 
so short-range Coulombic energies might tell you something.  But if you try to 
claim some energy of a specific interaction, it would be unphysical.


-Justin


interaction,is there any possibility to know the energy involved in the
process



--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] pdb2gmx error after switching force fields

[Justin Lemkul]

On 5/13/16 10:49 AM, Irem Altan wrote:

Hi,

I have a .pdb file that I’ve used in simulations with amber99sb before. I have 
recently switched to amber03. When I do pdb2gmx, I get the following warning:

WARNING: WARNING: Residue 26 named GLY of a molecule in the input file was 
mapped
to an entry in the topology database, but the atom CB used in
an interaction of type dihedral in that entry is not found in the
input file. Perhaps your atom and/or residue naming needs to be
fixed.



There is an error in the AMBER03 .rtp file.  Either delete the dihedral that 
calls for CB or upgrade your GROMACS version.  I fixed this nearly two years 
ago, so you're using something really outdated :)



The same thing is repeated for a number of residues (26, 51, 59, 66, 67, 83, 
85, 95). The weird thing is, the residue numbers in the pdb file start from 
107, and gmx complains about lower numbers. Also, have I understood correctly 
that gmx complains that glycines in my input file don’t have beta carbons? What 
could be the problem here?



pdb2gmx uses its own internal numbering, starting from 1.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] pdb2gmx error after switching force fields

[Irem Altan]

Hi,

I have a .pdb file that I’ve used in simulations with amber99sb before. I have 
recently switched to amber03. When I do pdb2gmx, I get the following warning:

WARNING: WARNING: Residue 26 named GLY of a molecule in the input file was 
mapped
to an entry in the topology database, but the atom CB used in
an interaction of type dihedral in that entry is not found in the
input file. Perhaps your atom and/or residue naming needs to be
fixed.

The same thing is repeated for a number of residues (26, 51, 59, 66, 67, 83, 
85, 95). The weird thing is, the residue numbers in the pdb file start from 
107, and gmx complains about lower numbers. Also, have I understood correctly 
that gmx complains that glycines in my input file don’t have beta carbons? What 
could be the problem here?

Best,
Irem
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Re: [gmx-users] Gromacs installation.

[Szilárd Páll]

With that amount of information it'll be hard for anyone to diagnose your
issue -- unless someone else ran into the same problem. If you want help
you need to i) try hard ii) try harder iii) describe what you tried and you
failed.

--
Szilárd

On Fri, May 13, 2016 at 12:53 PM, Elsaid Younes  wrote:

> Hi all,
>
> I have installed gromacs like the quick and dirty installation. I have a
> 16.04 version of ubuntu. I can not start it.
> I used to do the same procedure in ubuntu 15.10, and it worked fine.
>
> /Elsaid
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Re: [gmx-users] Hydrophobic interaction analysis

[Nikhil Maroli]

We can analyse hydrogen bond numbers, what about total hydrogen bond 
energy between two molecules over time like that in case of hydrophobic 
interaction,is there any possibility to know the energy involved in the 
process  

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Re: [gmx-users] Re. Generating topology for Tetrahydrofolate within CHARMM ff

[Justin Lemkul]

On 5/13/16 5:04 AM, zeineb SI CHAIB wrote:





@ Justin

Dear Justin,

Thank you very much for the website.

I tried to generate my topology from the website. After many problems in my input 
file, it finally generated the .str file with no error/warnings found but 
unfortunately some penalties were not good at all (> 50 and between 10 and 50)!

How can I fix the file?


'https://cgenff.paramchem.org/initguess/#20160513/THF_zinc_4228237.str'




You'll need to manually parametrize/refine anything that has bad penalties.

Spend some time with the CGenFF paper and tutorial:

http://dogmans.umaryland.edu/~kenno/cgenff/download.php
http://www.cecam.org/upload/files/file_1187.pdf

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Hydrophobic interaction analysis

[Sun Iba]

hi
Its hydrophobic effect, Nikhil. And you can make index of hydrophobic
groups in your protein, then calculate distance between them.

On Thu, May 12, 2016 at 11:03 PM, Nikhil Maroli  wrote:

> Dear all,
>
> is there any option in gromacs to study the hydrophobic interaction between
> the two molecule over the simulation time !
> --
> Ragards,
> Nikhil Maroli
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[gmx-users] Gromacs installation.

[Elsaid Younes]

Hi all,

I have installed gromacs like the quick and dirty installation. I have a
16.04 version of ubuntu. I can not start it.
I used to do the same procedure in ubuntu 15.10, and it worked fine.

/Elsaid
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[gmx-users] Re. Generating topology for Tetrahydrofolate within CHARMM ff

[zeineb SI CHAIB]

@ Justin

Dear Justin, 

Thank you very much for the website. 

I tried to generate my topology from the website. After many problems in my 
input file, it finally generated the .str file with no error/warnings found but 
unfortunately some penalties were not good at all (> 50 and between 10 and 50)! 

How can I fix the file?


'https://cgenff.paramchem.org/initguess/#20160513/THF_zinc_4228237.str' 


Thank you very much for your help. 

Zeineb. 


  
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Re: [gmx-users] Generating topology for a HEM protein with CHARMM27

[zeineb SI CHAIB]

@ Justin

Dear Justin, 

Thank you very much for your orientation and help. 

I visited CHARMM-GUI website and I found interesting tutorials for my 
HEM-protein but before going further I would like to know if it's feasible to 
use CHARMM GUI for my Hem-Protein and  include after my substrate (amino-acide) 
and a cofactor (Tetrahydrofolat) If yes, How can I do it? Any advices, tipes?  
After all, my goal is to simulate this hole system on GROMACS. 

NB: I also have problems with generating the topology of tetrahydrofolate from 
the website that you recommended 
'https://cgenff.paramchem.org/initguess/#20160513/THF_zinc_4228237.str' in a 
another post and I just added a comment)).


Thank you very much for your help. 

Zeineb. 


  
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Re: [gmx-users] Making separate topology file for QM atoms (bharat gupta)

[Groenhof, Gerrit]

You need to make one topology for your protein that includes all atoms that you 
want to treat with QM. If your QM region includes part of the protein and the 
ligand, you can most easily make one topology with the -merge option of pdb2gmx.

Gerrit

Dear Gromacs Users,

I am interested to know how to create a separate topology file for the QM
atoms of a system. It would be of great help if somebody can explain this.

For my QM system, I need to include the active site residues + ligand.

--
*Best Regards*
BM


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Re: [gmx-users] REMD error

[Mark Abraham]

Hi,

If you've configured with GMX_MPI, then the resulting GROMACS binary is
called gmx_mpi, so mpirun -np X gmx_mpi mdrun -multi ...

Mark

On Fri, May 13, 2016 at 10:09 AM YanhuaOuyang <15901283...@163.com> wrote:

> Hi,
> I have installed the openmpi 1.10, and I can run mpirun. When I installed
> grimaces 5.1, I configured -DGMX_MPI=on.
> And the error still happens .
> > 在 2016年5月13日，下午3:59，Mark Abraham  写道：
> >
> > Hi,
> >
> > Yes. Exactly as the error message says, you need to compile GROMACS
> > differently, with real MPI support. See
> >
> http://manual.gromacs.org/documentation/5.1.2/user-guide/mdrun-features.html#running-multi-simulations
> >
> > Mark
> >
> > On Fri, May 13, 2016 at 9:47 AM YanhuaOuyang <15901283...@163.com>
> wrote:
> >
> >> Hi,
> >> I am running a REMD of a protein, when I submit "gmx mdrun -s
> >> md_0_${i}.tpr -multi 46 -replex 1000 -reseed -1", it fails as the below
> >> Fatal error:
> >> mdrun -multi or -multidir are not supported with the thread-MPI library.
> >> Please compile GROMACS with a proper external MPI library.
> >> I have installed the openmpi  and gromacs 5.1.
> >> Do anyone know the problem.
> >>
> >> yours sincerelly,
> >> Ouyang
> >> --
> >> Gromacs Users mailing list
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> >> posting!
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Re: [gmx-users] REMD error

[YanhuaOuyang]

Hi,
I have installed the openmpi 1.10, and I can run mpirun. When I installed 
grimaces 5.1, I configured -DGMX_MPI=on.
And the error still happens .
> 在 2016年5月13日，下午3:59，Mark Abraham  写道：
> 
> Hi,
> 
> Yes. Exactly as the error message says, you need to compile GROMACS
> differently, with real MPI support. See
> http://manual.gromacs.org/documentation/5.1.2/user-guide/mdrun-features.html#running-multi-simulations
> 
> Mark
> 
> On Fri, May 13, 2016 at 9:47 AM YanhuaOuyang <15901283...@163.com> wrote:
> 
>> Hi,
>> I am running a REMD of a protein, when I submit "gmx mdrun -s
>> md_0_${i}.tpr -multi 46 -replex 1000 -reseed -1", it fails as the below
>> Fatal error:
>> mdrun -multi or -multidir are not supported with the thread-MPI library.
>> Please compile GROMACS with a proper external MPI library.
>> I have installed the openmpi  and gromacs 5.1.
>> Do anyone know the problem.
>> 
>> yours sincerelly,
>> Ouyang
>> --
>> Gromacs Users mailing list
>> 
>> * Please search the archive at
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>> posting!
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>> 
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Re: [gmx-users] REMD error

[Mark Abraham]

Hi,

Yes. Exactly as the error message says, you need to compile GROMACS
differently, with real MPI support. See
http://manual.gromacs.org/documentation/5.1.2/user-guide/mdrun-features.html#running-multi-simulations

Mark

On Fri, May 13, 2016 at 9:47 AM YanhuaOuyang <15901283...@163.com> wrote:

> Hi,
> I am running a REMD of a protein, when I submit "gmx mdrun -s
> md_0_${i}.tpr -multi 46 -replex 1000 -reseed -1", it fails as the below
> Fatal error:
> mdrun -multi or -multidir are not supported with the thread-MPI library.
> Please compile GROMACS with a proper external MPI library.
> I have installed the openmpi  and gromacs 5.1.
> Do anyone know the problem.
>
> yours sincerelly,
> Ouyang
> --
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[gmx-users] REMD error

[YanhuaOuyang]

Hi,
I am running a REMD of a protein, when I submit "gmx mdrun -s md_0_${i}.tpr 
-multi 46 -replex 1000 -reseed -1", it fails as the below
Fatal error:
mdrun -multi or -multidir are not supported with the thread-MPI library. Please 
compile GROMACS with a proper external MPI library.
I have installed the openmpi  and gromacs 5.1.
Do anyone know the problem.

yours sincerelly,
Ouyang
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Re: [gmx-users] REMD on more than one node

[Mark Abraham]

Hi,

You'll need to choose a replica setup that naturally fits on your available
hardware. Number of nodes * number of cores per node must equal number of
replicas * number of cores per replica. See also
http://manual.gromacs.org/documentation/5.1.2/user-guide/mdrun-features.html#running-multi-simulations

Mark

On Fri, May 13, 2016 at 4:41 AM YanhuaOuyang <15901283...@163.com> wrote:

> Hi,
> I am running a REMD with grimacs 5.0, I have 46 replica, 4 nodes, 16 cores
> per node. how can I use my compute resource and what’s the command of “gmx
> mdrun”?
> the command is below, I am not sure weather it is right
> mpirun -np 4 -npme gmx mdrun -s md_01.tpr  -multi 46 -replex 500 -reseed
> -1.
> mpirun -np 4 -npme gmx mdrun -s md_02.tpr  -multi 46 -replex 500 -reseed
> -1.
> mpirun -np 4 -npme gmx mdrun -s md_03.tpr  -multi 46 -replex 500 -reseed
> -1.
> …
> mpirun -np 4 -npme gmx mdrun -s md_46.tpr  -multi 46 -replex 500 -reseed
> -1.
>
>
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[gmx-users] PME and particle insertion

[Jakob Wohlert]

Dear all,

I see that issues concerning PME and particle insertions have been discussed 
before, and some issues were apparently resolved for the latest (5.1.2) 
version. However, I have noticed a strange thing when using TPI for inserting 
(tip3p) water in liquid water at 300 K and 1 atm; the distribution of DU using 
PME becomes very different from when using a plain cutoff. Using reaction field 
electrostatics on the other hand gives a distribution which looks essentially 
the same as for cutoffs. You can have a look at the distributions at: 
http://www.wohlert.se/insrun.png

The reported chemical potentials also differ; cutoff and RF give reasonable 
, but with PME they differ by an order of magnitude. I also tried using 
water at lower density where convergence shouldn't be an issue, and basically 
got the same effect: http://www.wohlert.se/insrun2.png

I would of course expect some difference between PME and plain cutoffs, but 
this seems unreasonable to me. Or isn’t it?

Any suggestion what’s going on would be appreciated!

Regards,
Jakob

PS
I use gmx 5.1.2, with 7000 tip3p water in cubic box, and the mdp file looks as 
below, with the only difference between the runs is that coulomb type is either 
cut-off, PME, or Reaction-field.

integrator   = tpi
dt   = 0.002
nsteps   = 10
comm_mode= Linear
comm_grps= System
nstcomm  = 1
pbc  = xyz

nstlist  = 1
ns_type  = grid
rlist= 1.2
cutoff-scheme = group

coulombtype  = Cut-off
rcoulomb = 1.2
vdw-type = Cut-off
rvdw = 1.2
epsilon-rf  = 80

Tcoupl   = berendsen
tc-grps  = System
tau_t= 2.0
ref_t= 300
ld_seed  = -1

Pcoupl   = no

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[gmx-users] Regarding Dynamic cross correlation map analysis

[soumi]

Hi,I am working on MD studies of Protein-DNA complex.I get 
trajectories from gromacs version 5.1 . NowI want to form dynamic cross 
correlation mapfrom thesetrajectories.Please let me know 
which software can read .trr file and I can use to 
plotDynamic cross correlation map.I have read VMD tutorial 
onDynamical Network Analysis .Here psf and dcd files have been used to 
create the network.My question is :Is it possible to doDynamical Network 
Analysis using VMD through GROMACStrajectories?With Regards,Soumi Das
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