Re: [gmx-users] QUERY IN GRO FILE

[amitbehra]

Hi,
Yeah, both confout.gro and em.gro are same for the same tpr input file.
The -deffnm flag is to indicate the names you want to give to your output
files. Incase the -deffnm flag is missing GROMACS gives default names.

Regards,
Amit Behera
REsearch Scholar,
IISc, Bangalore.
> --
>
> Message: 3
> Date: Thu, 30 Mar 2017 11:23:03 +0530
> From: Neha Gupta 
> To: gmx-us...@gromacs.org
> Subject: [gmx-users] QUERY IN GRO FILE
> Message-ID:
>   
> Content-Type: text/plain; charset=UTF-8
>
> Hi gromacs users,
>
>
> I have a doubt in this command,
>
> grompp -f em.mdp -c conf.gro -p topol.top -o em

the output file from grompp command should be tpr. so it should be " -o
em.tpr" because mdrun will take that tpr file as input.

> mdrun -v -deffnm em
>
>
> These commands generate em.gro, em.tpr, em.trr, em.log file.
>
>
> There is another command which is
>
>
> mdrun -s em.tpr
>
> which generates confout.gro
>
> Does em.gro and confout.gro are one and the same?
>
> What are the technical differences?
>
>
> Thanks,
>
> Neha
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[gmx-users] mdrun error

[amitbehra]

Hello,
After equilibrating my system for 100 ns( during which there was restraint
on the protein letting the lipids to equilibrate), when I am trying to run
my unrestrained run I am getting the following errors:
1. "bonds that rotated more than 30 degree"
2. "1 particles communicated to PME rank 0 are more than 2/3 times the
cut-off out of the domain decomposition cell of their charge group in
dimension x"
3. "Listed nonbonded interaction between particles 71916 and 71920
at distance 5.535 which is larger than the table limit 2.215 nm."

What might be the reason for this error. I thought 100ns is enough for
equilibration.

Thanks,
Amit Behera
Research Scholar,
IISc.

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[gmx-users] gmx wheel

[amitbehra]

Hello,
I am trying to create a helical wheel. The format of .dat file is:

No. of residues
Names of the residues

But it is giving error:
Incorrect usage of option -f

Can anyone help me with correct format ?

Regards,
Amit Behera

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[gmx-users] Plumed with GROMACS 5.1.2

[amitbehra]

Hello,
I have installed plumed 2.3. But I am having doubt in the patching process.
Where should I patch the executable? Do I need to recompile gromacs after
patching ?

Thanks
Amit Behera

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[gmx-users] GROMACS 4.6.4 vs GROMACS 5.1.2

[amitbehra]

Is there any major changes from version 4.* to 5.* that affects the
stability of the a protein-lipid system ?
I have been using GROMACS 5.1.2 but recently I got to know that GROMACS
5.1.* has some changes which affects long range LJ calculations which was
not there in GROMACS 4.* .
Can anyone help me out of this dilemma of which version is more accurate
to simulate a trans-membrane helical protein?

Reagrds,
Amit Behera
Research Scholar
IISc

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Re: [gmx-users] Unstable Alpha Helix

[amitbehra]

Hello Justin,
I am using "stride" program to analyze the helices.
Can the Potential switch and other mdp parameters affect the stability of
an Alphahelix.

Regards,
Amit
> Date: Mon, 19 Dec 2016 08:06:29 -0500
> From: Justin Lemkul 
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Unstable Alpha Helix
> Message-ID: <78b951a1-4cb3-e4fc-4239-cc19fd03c...@vt.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> On 12/19/16 7:01 AM, amitbe...@chemeng.iisc.ernet.in wrote:
>> Hello everyone,
>> I am trying to simulate an Alpha helix inside a bilayer. But a part of
>> the
>> alpha helix is loosing its form and converting into turns( while
>> alphahelix should be stable in the bilayer environment)
>
> How are you assessing this?  DSSP?  Dihedral time series?  Note that
> simple
> visualization is often misleading.  Helices can still be helices, even if
> the
> program you're looking at disagrees.
>
> -Justin
>
>> I am using Amber-99sb-ILDN for the protein and Slipids for the bilayer.
>> I am using Potential-switch for VdW and PME for electrostatics.
>> Does these parameters affect the form of the Alphahelix ?
>>
>> Regards,
>> Amit
>>
>
> --
> ==
>
> 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] Unstable Alpha Helix

[amitbehra]

Hello everyone,
I am trying to simulate an Alpha helix inside a bilayer. But a part of the
alpha helix is loosing its form and converting into turns( while
alphahelix should be stable in the bilayer environment)
I am using Amber-99sb-ILDN for the protein and Slipids for the bilayer.
I am using Potential-switch for VdW and PME for electrostatics.
Does these parameters affect the form of the Alphahelix ?

Regards,
Amit

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[gmx-users] gmx genrestr

[amitbehra]

Hello,
I generated a distance matrix for C-alpha of the protein. I included in
.top file too. But still when I am running grompp there is an error:
NOTE 2 [file unknown]:
  disre = no, removed 45753 distance restraints
Do I need to change anything else apart from justchanging the "define"
parameter in the mdp file ?

Thanks,
Amit Behera

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[gmx-users] keeping the pitch of helix constant

[amitbehra]

Hello,
Is there any way in GROMACS-5.1.2 to keep the pitch of an alpha helix
constrained.

Regards,
Amit

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[gmx-users] gmx do_dssp

[amitbehra]

Hello,
Does the gmx do_dssp command works with dssp version 2.2.1 ?

Regards,
Amit

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[gmx-users] GROMACS-5.1.4 vs. GROMACS-5.1.2

[amitbehra]

Hello Everyone,
I was initially using GROMACS-5.1.2. But in my institute cluster they have
recently installed GROMACS-5.1.4.
I just wanted to know will there be any difference in result between these
two versions.

Regards,
Amit Behera

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[gmx-users] LINCS warning

[amitbehra]

Hello users,
I was trying to energy minimize my system of protein embedded in bilayer.
But I am receiving the following error:

Step -1, time -0.001 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000942, max 0.149038 (between atoms 21616 and 21619)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length

Steepest Descents:
   Tolerance (Fmax)   =  1.0e+03
   Number of steps=   50

Energy minimization has stopped, but the forces have not converged to the
requested precision Fmax < 1000 (which may not be possible for your system).
It stopped because the algorithm tried to make a new step whose size was too
small, or there was no change in the energy since last step. Either way, we
regard the minimization as converged to within the available machine
precision, given your starting configuration and EM parameters.

Double precision normally gives you higher accuracy, but this is often not
needed for preparing to run molecular dynamics.
You might need to increase your constraint accuracy, or turn
off constraints altogether (set constraints = none in mdp file)

writing lowest energy coordinates.

Steepest Descents converged to machine precision in 11 steps,
but did not reach the requested Fmax < 1000.
Potential Energy  =  2.3557852e+30
Maximum force =inf on atom 34347
Norm of force =inf

what approach should I use to get rid of this problem?

Regards,
Amit Behera


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Re: [gmx-users] pdb2gmx

[amitbehra]

Hi Justin,
Here is the full screen output:

Read 2236 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
There are 1 chains and 0 blocks of water and 285 residues with 2236 atoms

  chain  #res #atoms
  1 ' '   285   2236

All occupancies are one
Opening force field file
/usr/local/gromacs/share/gromacs/top/amber99sb-ildn.ff/atomtypes.atp
Atomtype 67
Reading residue database... (amber99sb-ildn)
Opening force field file
/usr/local/gromacs/share/gromacs/top/amber99sb-ildn.ff/aminoacids.rtp
Residue 93
Sorting it all out...
Opening force field file
/usr/local/gromacs/share/gromacs/top/amber99sb-ildn.ff/dna.rtp
Residue 109
Sorting it all out...
Opening force field file
/usr/local/gromacs/share/gromacs/top/amber99sb-ildn.ff/rna.rtp
Residue 125
Sorting it all out...
Opening force field file
/usr/local/gromacs/share/gromacs/top/amber99sb-ildn.ff/aminoacids.hdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/amber99sb-ildn.ff/dna.hdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/amber99sb-ildn.ff/rna.hdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/amber99sb-ildn.ff/aminoacids.n.tdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/amber99sb-ildn.ff/aminoacids.c.tdb

Back Off! I just backed up topol.top to ./#topol.top.4#
Processing chain 1 (2236 atoms, 285 residues)
Analysing hydrogen-bonding network for automated assignment of histidine
 protonation. 412 donors and 445 acceptors were found.
There are 574 hydrogen bonds
Will use HISE for residue 292
Identified residue LYS8 as a starting terminus.
Identified residue HIS292 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Special Atom Distance matrix:
   MET70   CYS87  MET270  MET281  CYS285
   SD500   SG649  SD2051  SD2135  SG2165
   CYS87   SG649   2.813
  MET270  SD2051   5.200   2.414
  MET281  SD2135   3.579   0.855   1.703
  CYS285  SG2165   3.012   0.370   2.301   0.930
  HIS292 NE22232   1.990   1.007   3.388   1.772   1.152
Opening force field file
/usr/local/gromacs/share/gromacs/top/amber99sb-ildn.ff/aminoacids.arn
Opening force field file
/usr/local/gromacs/share/gromacs/top/amber99sb-ildn.ff/dna.arn
Opening force field file
/usr/local/gromacs/share/gromacs/top/amber99sb-ildn.ff/rna.arn
Checking for duplicate atoms
Generating any missing hydrogen atoms and/or adding termini.

---
Program gmx pdb2gmx, VERSION 5.1.2
Source code file:
/home/amit/Documents/gromacs-5.1.2/src/gromacs/gmxpreprocess/pgutil.c,
line: 127

Fatal error:
Residue 1 named LYS of a molecule in the input file was mapped
to an entry in the topology database, but the atom CA used in
that entry is not found in the input file. Perhaps your atom
and/or residue naming needs to be fixed.

>>
>> Message: 7
>> Date: Fri, 19 Aug 2016 15:30:14 -0400
>> From: Justin Lemkul 
>> To: gmx-us...@gromacs.org
>> Subject: Re: [gmx-users] pdb2gmx
>> Message-ID: 
>> Content-Type: text/plain; charset=windows-1252; format=flowed
>>
>>
>>
>> On 8/19/16 10:52 AM, amitbe...@chemeng.iisc.ernet.in wrote:
>>> Hello users,
>>> I am using pdb2gmx on a protein.
>>> Fatal error:
>>> Residue 1 named LYS of a molecule in the input file was mapped
>>> to an entry in the topology database, but the atom N used in
>>> that entry is not found in the input file. Perhaps your atom
>>> and/or residue naming needs to be fixed.
>>>
>>> ATOM  1  N   LYS 8  59.565  44.696  51.226  1.00  0.00
>>>   N
>>> 0.00   H
>>> ATOM 19  NZ  LYS 8  62.201  50.111  51.767  1.00  0.00
>>>   N
>>>
>>> These are N atoms in my LYS . Can anyone point out what the problem.
>>>
>>
>> Please provide your exact pdb2gmx command and the full screen output.
>>
>> -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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> End of gromacs.org_gmx-users Digest, Vol 148, Issue 79
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Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 148, Issue 78

[amitbehra]

Hello Justin,
I used gmx pdb2gmx -f protein.pdb -o protein.gro -ignh

and I got the error:
Program gmx pdb2gmx, VERSION 5.1.2
Source code file:
/home/amit/Documents/gromacs-5.1.2/src/gromacs/gmxpreprocess/pgutil.c,
line: 127

Fatal error:
Residue 1 named LYS of a molecule in the input file was mapped
to an entry in the topology database, but the atom N used in
that entry is not found in the input file. Perhaps your atom
and/or residue naming needs to be fixed.

Regards,
Amit Behera

> --
>
> Message: 7
> Date: Fri, 19 Aug 2016 15:30:14 -0400
> From: Justin Lemkul 
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] pdb2gmx
> Message-ID: 
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> On 8/19/16 10:52 AM, amitbe...@chemeng.iisc.ernet.in wrote:
>> Hello users,
>> I am using pdb2gmx on a protein.
>> Fatal error:
>> Residue 1 named LYS of a molecule in the input file was mapped
>> to an entry in the topology database, but the atom N used in
>> that entry is not found in the input file. Perhaps your atom
>> and/or residue naming needs to be fixed.
>>
>> ATOM  1  N   LYS 8  59.565  44.696  51.226  1.00  0.00
>>   N
>> 0.00   H
>> ATOM 19  NZ  LYS 8  62.201  50.111  51.767  1.00  0.00
>>   N
>>
>> These are N atoms in my LYS . Can anyone point out what the problem.
>>
>
> Please provide your exact pdb2gmx command and the full screen output.
>
> -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

[amitbehra]

Hello users,
I am using pdb2gmx on a protein.
Fatal error:
Residue 1 named LYS of a molecule in the input file was mapped
to an entry in the topology database, but the atom N used in
that entry is not found in the input file. Perhaps your atom
and/or residue naming needs to be fixed.

ATOM  1  N   LYS 8  59.565  44.696  51.226  1.00  0.00
  N
0.00   H
ATOM 19  NZ  LYS 8  62.201  50.111  51.767  1.00  0.00
  N

These are N atoms in my LYS . Can anyone point out what the problem.

Regards,
Amit

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[gmx-users] Equilibration problem

[amitbehra]

Hello everyone,
I prepared a bilayer using PACKMOL. Then ran energy minimisation. Till
this point the structure completely intact. Then I ran nvt on the
structure. At this point GROMACS-5.1.2 is giving back more than one pdb
files (named step**.pdb) instead of usual .gro file.
Does anyone know how to solve this issue.

Thanks
Amit Behera

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[gmx-users] electron density by gmx density

[amitbehra]

Hello Users,
I was wandering how can we calculate the electron density with the help of
gmx density. how to write the " -ei [<.dat>] (electrons.dat) "

Regards,
Amit Behera

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[gmx-users] GRID-MAT- area per lipid calculation

[amitbehra]

Hello Justin,
I was trying to calculate area per lipid using GridMAT. But its giving
back me the error :
" Illegal division by zero at GridMAT-MD.pl line 761 "
Can you help in finding the root of this error ? The bilayer just consists
of one type of lipid and sol.

Regards,
Amit Behera

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[gmx-users] Regarding periodic boundary condition

[amitbehra]

Hello,
After a run usually the molecules seems to be broken due to PBC . Do I
need to convert this .gro file into another .gro file with whole molecule(
using trjconv) before the next step. Will there be any difference in
simulation results ?

Regards,
Amit Behera

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[gmx-users] gmx distance

[amitbehra]

Hello users,
I wanted to calculate Oxygen-Oxygen pair distance of a simple bulk water
simulation. I made group of all the oxygen atoms using make_ndx.
Now I am trying to use " gmx distance" :
gmx distance -f water_whole.xtc -s water.tpr -n index.ndx -oav
distances_oo.xvg
But this is giving wrong output.
Can anyone help me in how to properly use gmx distance ???

Regards,
Amit Behera


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[gmx-users] replacing lipid molecules with cholesterol

[amitbehra]

Hello,
I built a system of lipid bilayer. Now I want to replace some of the lipid
molecules by cholesterol molecules. Can anyone help me out in how to do
that.

Regards,
Amit Behera
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[gmx-users] SETTLE constraint

[amitbehra]

Hello users,
I was going through a literature ( dx.doi.org/10.1021/ct300342n ). Here
they use GROMACS 4.5 version and use SETTLE constraint for bonds in water
I wanted to know how can I apply SETTLE method in GROMACS 5.1.2.

Regards,
Amit Behera
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[gmx-users] TRR file in VMD

[amitbehra]

Hello users,
When I am loading data (.trr) into my structure file (.gro) in VMD. The
trajectories are showing some kind of grid. It's like VMD is showing the
path of a trajectory with actual lines.
Can this problem be related to GROMACS-5.1.2 or do I need to change some
settings in VMD ?

Regards,
Amit Behera
Research Scholar,
IISc
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[gmx-users] gmx convert-tpr

[amitbehra]

Hello gmx_users,
I was running a simulation and the wall time got exceeded in the cluster.
I am thinking to use  gmx convert-tpr. -extend (time)
Does this method have any drawbacks. If so what other methods can I try to
resume my simulation.

Regards,


Amit Behera
Research Scholar
Dept. of Chemical Engineering,
IISc
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[gmx-users] Tutorial #3 : Umbrella Sampling (By Justin Lemkul)

[amitbehra]

Hello,
The summary_distances.dat file contains only one column ( the column for
COM is missing).
I am using GROMACS 5.1.2. How to solve this issue.

Regards,
Amit Behera
Research Scholar,
Dept. of Chemical Engineering,
IISc
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[gmx-users] gmx rdf

[amitbehra]

Hello gmx_users,
I was trying to plot distribution function in a bilayer system using gmx
rdf. I used the system as a reference ( thinking it will take the COM of
the system as reference point) . Then I plotted RDF of a marked atom. But
it is plotting only in the positive direction while the lipids in the
lower leaflet are also containing the marked atom. So I am unable to see
the distribution from center of the bilayer to the lower leaflet.
Can anyone please help me out in identifying my mistake.

Regards,
Amit Behera

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Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 146, Issue 59

[amitbehra]

Hi Sotirios,
What else should I check if I am trying to equilibrate a bilayer. Box size
and temperature is okay. Any suggestions on what other quantity i should
check ?

Thanks,
Amit Behera
> Message: 1
> Date: Mon, 13 Jun 2016 07:29:51 +
> From: "Sotirios Dionysios I. Papadatos" 
> To: Discussion list for GROMACS users 
> Subject: Re: [gmx-users] Is charmm GUI ideal for membrane building
> Message-ID:
>   
> 
>
> Content-Type: text/plain; charset="us-ascii"
>
> I might be wrong here, but energy is supposed to converge. Maybe you want
> to verify something else?

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Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 146, Issue 57

[amitbehra]

Hello,
Thanks Tsjerk for the reply.So the equilibration needs to be run for some
more time.
Can I incorporate other force field in the membrane built from Charmm-GUI
if the atom names are same in the forcefield as used by Charmm-GUI ?

Regards,
Amit Behera
Dept. of Chemical Engg.,
IISc.

> Date: Mon, 13 Jun 2016 06:44:03 +0200
> From: Tsjerk Wassenaar 
> To: Discussion list for GROMACS users 
> Subject: Re: [gmx-users] Is charmm GUI ideal for membrane building
> Message-ID:
>   
> Content-Type: text/plain; charset=UTF-8
>
> Hi Amit,
>
> What membrane and what time scale are you talking about? Complex membranes
> may take microseconds to equilibrate.
>
> Cheers,
>
> Tsjerk
> On Jun 13, 2016 06:13,  wrote:
>
>> Hello everyone,
>> I built a lipid membrane in Charmm-GUI and tried to equilibrate it in
>> GROMACS 5.1.2. But the total energy goes on decreasing. Is it normal or
>> should I try building the membrane by other methods.
>>
>> Thanks in advance,
>>
>> Amit Behera
>>

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[gmx-users] Is charmm GUI ideal for membrane building

[amitbehra]

Hello everyone,
I built a lipid membrane in Charmm-GUI and tried to equilibrate it in
GROMACS 5.1.2. But the total energy goes on decreasing. Is it normal or
should I try building the membrane by other methods.

Thanks in advance,

Amit Behera

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Re: [gmx-users] Umbrella Sampling (Justin Lemkul)

[amitbehra]

Hello all,
I was practicing the umbrella sampling tutorial by Dr. Justin Lemkul. In
my summary_distances.dat file there is only one column ( the column for
centre of mass is missing ).

Can anyone say what possible mistakes I must have done.

Regards,
Amit Behera
Dept. of Chemical Engg.,
IISc, India
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[gmx-users] Umbrella sampling Tutorial by Dr. Lemkul

[amitbehra]

Hello,
I was running the simulation for the umbrella sampling tutorial by Dr.
Justin Lemkul in GROMACS 5.1.2 and I followed the steps exactly as they
were mentioned.
But in my summary_distances.dat there is one column. the COM column is
missing. I am new to gromacs . So please help me out.

Regards,

Amit Behera,
Dept. of Chemical Engineering,
Indian Institute of Science, Bengaluru,
India.


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