[gmx-users] Grid Spacing

[Apramita Chand]

Dear All,
Which is more appropriate fourier grid spacing for gromos53a6 ff with
cutoffs being 0.9 and 1.4nm?
0.16 or 0.12??
I've not seen too many papers with 0.16 being used for this forcefield and
that too with cutoffs like 1.0 for rcoulomb and rvdw.

Is there any problem if I use fourier spacing of 0.16 with these
cutoffs(0.9,1.4)?

Also,should the grid spacing be same for equilibration and production runs??

Yours sincerely,
Apramita
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[gmx-users] Multiple output log. xtc .edr files generated using mpirun

[Abhishek Acharya]

Hello GROMACS users,

I am trying to run a simulation on a university cluster; I am using
gromacs-5.1.2. The problem is while running mdrun, using the following
command:

mpirun -np 32 gmx mdrun -s prod.tpr -deffnm prod_out -pin on   ### I
expected gmx mdrun_mpi here but it was not available.

I am getting multiple log files, xtc, edr files as the output and all the
log files say the following:


Running on 1 node with total 16 cores, 16 logical cores
Hardware detected:
  CPU info:
Vendor: GenuineIntel
Brand:  Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz
Family:  6  model: 45  stepping:  7
CPU features: aes apic avx clfsh cmov cx8 cx16 htt lahf_lm mmx msr
nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1
sse4.2 ssse3 tdt x2apic
SIMD instructions most likely to fit this hardware: AVX_256
SIMD instructions selected at GROMACS compile time: AVX_256

This in itself is pretty weird. I am guessing that the package is not
properly installed by the admin. My question is what is the exact problem
with the setup and what is the solution; i need to communicate this to the
admin. Although, I reported the issue previously, but it seems he doesn't
understand where the problem seems to be.


Thanks in advance.

Sincerely,
Abhishek Acharya
Research Associate,
Department of Molecular Nutrition
CSIR-Central Food Technological Research Institute,
Mysuru-570020
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Re: [gmx-users] Anybody using Silica InterfaceFF on Gromacs?

[Alex]

Sure - one should use a tool capable of doing the job, and use its optional
capabilities accordingly. Choosing non-bonded exclusions based on bonds, in
a way that does not implement the intended model physics, is indeed wrong,
but that doesn't make the use of modified 1-4 pair interactions "childish"
in general ;-)

You are correct. My point only holds in a situation where people indeed 
are doing that: using an inappropriate tool. And you see how many people 
on this list ask questions about doing solid-state simulations with 
Gromacs. I have a dual background and could give many examples where the 
use of what works for proteins/lipids in water is, well, childish, for 
lack of a better word in solid-state systems. I hope noone takes 
offense. :) The "problem" is that, thanks to your hard work, Gromacs is 
delightful to use, much more so than LAMMPS, and my hope is that one day 
you guys will just implement things like REBO and ReaxFF and MEAM, and 
Weber-Stillinger and what-not. If you do that, I will fly to your 
location, give you a hug, and personally buy you a steak dinner. In 
other words, my hope is that one day Gromacs will be an appropriate tool 
for all of classical MD, solid or liquid state.

So, for the record, the actual issue is that GROMACS does not implement
some kind of tapering of non-bonded interactions that would apply between
particle pairs at short range?

Within the question initially posed (about silica), Gromacs is fairly 
capable of everything necessary, it is just a matter of carefully 
reading the documentation on the original solid-state potential and then 
setting up the adopted forcefield, including the nrexl, etc. The much 
bigger issue (with solid-state things in general) is the springs for 
bonds, angles, etc, and use permanent molecular topologies. Wrong phonon 
spectra, wrong elastic properties away from 0K, wrong rippling spectra 
of graphene and likely all atomically thin membranes, inability to do 
covalent bond breaking/formation, etc, etc. That is, things Gromacs was 
never intended for. But then again, see what I said above.


Alex
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Re: [gmx-users] Can not open file: run.trr

[Mark Abraham]

Hi,

Use tools like rsync to do your file copies and preserve suitable
permissions automatically. And try to avoid copying files > 2GB to
partitions formatted in Windows-friendly fashion to e.g. FAT32 file sytems,
as external hard drives might be formatted.

Mark

On Sun, Jul 2, 2017 at 10:59 PM Samith Rathnayake 
wrote:

> Hi everyone,
>
> Recently I was run a 30ns gromacs simulation.And for the analysis part, i
> was copied down the entire file directory of the simulation into an
> external hard disk and shift it into another computer with same OS and same
> version of gromacs (ubuntu 14.04 and gromacs 4.6.5). After copied down to
> another computer, I was work with the file permission scenario by using the
> command: chmod 777 for every and each file .Then  I was run the g_rms
> command for the  RMSD analysis.But i was got the :
>
> 
> Program g_rms, VERSION 4.6.5
> Source code file: /build/buildd/gromacs-4.6.5/src/gmxlib/gmxfio.c, line:
> 524
>
> Can not open file:
> run70.trr
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
>
> ...
> The command worked with the same files when those files were in the
> previous (original location) computer.Even i arranged the file permission
> on the new computer (new space) the trr files cant open.
> How to overcome this situation?
>
>
> thank you in advance.
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> Gromacs Users mailing list
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Re: [gmx-users] Anybody using Silica InterfaceFF on Gromacs?

[Mark Abraham]

Hi,

On Fri, Jun 30, 2017 at 2:46 AM Alex  wrote:

> >
> >
> >>
> >> He he, childish :)
> >
> > David, no offense intended. I just think that when applied to solids, the
> entire concept of what works so well for biomolecular systems becomes a bit
> of a joke. And vice versa, to be fair. Spoken from experience, really -- we
> here used Gromacs to simulate things that I keep telling people not to
> simulate with Gromacs, and it got published!. :)
>

Sure - one should use a tool capable of doing the job, and use its optional
capabilities accordingly. Choosing non-bonded exclusions based on bonds, in
a way that does not implement the intended model physics, is indeed wrong,
but that doesn't make the use of modified 1-4 pair interactions "childish"
in general ;-)


> In any case, I second what was said above re: # of exclusions. Solid-state
> potentials use smooth drop-offs to exclude long-range interactions between
> close neighbor sharing elements, so looking into David's suggestion may in
> fact fix the issues immediately.
>

So, for the record, the actual issue is that GROMACS does not implement
some kind of tapering of non-bonded interactions that would apply between
particle pairs at short range?

Mark


> Alex
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Re: [gmx-users] Anybody using Silica InterfaceFF on Gromacs?

[Diez Fernandez, Amanda]

Hi,
I have now solved the problem.
I have added a list of the 1-4 pairs within [ Pairs ] and it has led to
the correct equilibrium bond length.
Just as reference, information on the forcefield I am using is found in
this paper: http://pubs.acs.org/doi/abs/10.1021/cm500365c
Cheers,
Amanda




On 30/06/2017, 01:46, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se
on behalf of gromacs.org_gmx-users-requ...@maillist.sys.kth.se"
 wrote:

>Send gromacs.org_gmx-users mailing list submissions to
>   gromacs.org_gmx-users@maillist.sys.kth.se
>
>To subscribe or unsubscribe via the World Wide Web, visit
>   https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
>or, via email, send a message with subject or body 'help' to
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>When replying, please edit your Subject line so it is more specific
>than "Re: Contents of gromacs.org_gmx-users digest..."
>
>
>Today's Topics:
>
>   1. Re: NoPbc (Mark Abraham)
>   2. Re: RemvingDummyAtoms (Mark Abraham)
>   3. Re: gromacs.org_gmx-users Digest, Vol 158, Issue 186 (Thanh Le)
>   4. Re: gromacs.org_gmx-users Digest, Vol 158, Issue 186
>  (Mark Abraham)
>   5. Re: gromacs.org_gmx-users Digest, Vol 158, Issue 186
>  (Mark Abraham)
>   6. Re: Anybody using Silica InterfaceFF on Gromacs? (Alex)
>
>
>--
>
>Message: 1
>Date: Thu, 29 Jun 2017 22:12:46 +
>From: Mark Abraham 
>To: gmx-us...@gromacs.org
>Subject: Re: [gmx-users] NoPbc
>Message-ID:
>   
>Content-Type: text/plain; charset="UTF-8"
>
>On Thu, Jun 29, 2017 at 7:29 PM Mostafa Javaheri
>
>wrote:
>
>> Dear gmx users
>>
>> I'm doing QM/MM simulation by using ORCA-Gromacs interface, the whole
>> simulation will take only 1 ps and I need to set pbc off. For this short
>> period of simulation does the pressure of the box change?
>
>
>There's no box if pbc is off. What would its walls be made of? Thus, no
>external pressure.
>
>
>> Does the water
>> vaporize after 500 steps? Any helps will be appreciated.
>>
>
>Water will start to evaporate, but probably not noticeable in that time
>frame. Run a classical MD with the same setup for 1 ps on just a globule
>of
>water to see.
>
>Mark
>
>
>> Regards
>>
>> M.Javaheri
>> --
>> 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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>> send a mail to gmx-users-requ...@gromacs.org.
>>
>
>
>--
>
>Message: 2
>Date: Thu, 29 Jun 2017 22:13:36 +
>From: Mark Abraham 
>To: gmx-us...@gromacs.org
>Subject: Re: [gmx-users] RemvingDummyAtoms
>Message-ID:
>   
>Content-Type: text/plain; charset="UTF-8"
>
>Hi,
>
>gmx trjconv can apply a selection (e.g. generated with gmx select) to your
>trajectory frames. gmx convert-tpr can do the same to your tpr, which you
>might need to help analysis work later on.
>
>Mark
>
>On Thu, Jun 29, 2017 at 10:57 PM Mostafa Javaheri <
>javaheri.grom...@gmail.com> wrote:
>
>> Dear gmx users
>>
>> I really appreciate it if anyone could tell me how could I remove dummy
>> atoms from my trajectory? I made them before running the simulation for
>> adding repulsive potential and now for analyzing the results there is no
>> need for them.
>>
>> Regards
>>
>> M.Javaheri
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
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>> posting!
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>> send a mail to gmx-users-requ...@gromacs.org.
>>
>
>
>--
>
>Message: 3
>Date: Thu, 29 Jun 2017 15:20:44 -0700
>From: Thanh Le 
>To: gromacs.org_gmx-users@maillist.sys.kth.se
>Subject: Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 158, Issue
>   186
>Message-ID: 
>Content-Type: text/plain;  charset=us-ascii
>
>Hi Mr. Abraham.
>My system is quite small, only about 8000 atoms. I have run this system
>for 100 ns, which took roughly about 2 days. Hence, a run of 1
>microsecond would take about 20 days. I am trying to shorten it down to 2
>days by using more than 1 node.
>Thanks,
>Thanh Le
>> On Jun 29, 2017, at 3:10 PM,
>>gromacs.org_gmx-users-requ...@maillist.sys.kth.se wrote:
>> 
>>> http://www.gromacs.org/Support/Mailing_Lists
>>>
>
>
>--
>
>Message: 4
>Date: Thu, 29 Jun 2017 22:37:54 +
>From: Mark Abraham 
>To: gmx-us...@gromacs.org, gromacs.org_gmx-users@maillist.sys.kth.se
>Subject: Re: [gmx-users]

[gmx-users] Difference between semi isotropic coupling and surface tension option

[Ali Shomali]

Dear all Gromacs users

I'm simulating a monolayer at water/vacuum interface with Gromacs and I'm
studying surface tension and area per lipid variations. the problem that is
very confusing me on this subject is that when I use semiisotropic option
to impose a negative lateral pressure and so a specific surface tension ,
my final area per lipid is very different from surface tension option but
when I use my energy files, both of them (surface tension or semiisotropic
output) are resulted in a very same  surface tensions.so how is it possible
that the same surface tension gives different area per lipids? if the
procedures are different, which one is more accurate?
I appreciate your kind and helpful advises.
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[gmx-users] Can not open file: run.trr

[Samith Rathnayake]

Hi everyone,

Recently I was run a 30ns gromacs simulation.And for the analysis part, i
was copied down the entire file directory of the simulation into an
external hard disk and shift it into another computer with same OS and same
version of gromacs (ubuntu 14.04 and gromacs 4.6.5). After copied down to
another computer, I was work with the file permission scenario by using the
command: chmod 777 for every and each file .Then  I was run the g_rms
command for the  RMSD analysis.But i was got the :

Program g_rms, VERSION 4.6.5
Source code file: /build/buildd/gromacs-4.6.5/src/gmxlib/gmxfio.c, line: 524

Can not open file:
run70.trr
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

...
The command worked with the same files when those files were in the
previous (original location) computer.Even i arranged the file permission
on the new computer (new space) the trr files cant open.
How to overcome this situation?


thank you in advance.
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[gmx-users] Issue with the PDB generated after topology

[Khadija Amine]

Dear Mark,

Thank you for your reply.

My starting pdb sequence on pymol is: A 1-166, B 54-131

After topology generation and solvation, I can display the whole structure
with the two chains A and B but in terms of sequence, the chain B is absent.

Please, let me know if any further information needed.

Khadija


*Khadija Amine*
Ph.D. Biology and Health
Biochemistry & Bioinformatics
Phone: 9584
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Re: [gmx-users] Nano-structures equilibration

[Alex]

You have problems with the system and you expect everyone here to be a 
magician and guess your inputs. What is the forcefield, what is the 
timestep, how are you describing your graphene sample, what is your 
number of exclusions for that sample, what is your barostat type during 
eqilibration? Are you doing static energy minimization prior to your 
equilibration run?


Alex


On 7/1/2017 11:58 PM, ‪Mohammad Roostaie‬ ‪ wrote:

Thank you very much, Alex. I also performed the process on GPU, and I got the 
below error:
step 1: Water molecule starting at atom 96743 can not be settled.Check for bad 
contacts and/or reduce the timestep if appropriate.Wrote pdb files with 
previous and current coordinates
WARNING: Listed nonbonded interaction between particles 4321 and 4328at 
distance 21.231 which is larger than the table limit 1.853 nm.
This is likely either a 1,4 interaction, or a listed interaction insidea 
smaller molecule you are decoupling during a free energy calculation.Since 
interactions at distances beyond the table cannot be computed,they are skipped 
until they are inside the table limit again. You willonly see this message 
once, even if it occurs for several interactions.
IMPORTANT: This should not happen in a stable simulation, so there isprobably 
something wrong with your system. Only change the table-extensiondistance in 
the mdp file if you are really sure that is the reason.
I would appreciate any help.
Regards,Mohammad

   From: Alex 
  To: gmx-us...@gromacs.org
  Sent: Friday, 30 June 2017, 22:21:26
  Subject: Re: [gmx-users] Nano-structures equilibration
   
You have performance-related errors, maybe try a different number of

ranks, or another machine, or OpenMP instead of MPI -- hope others will
be able to comment on technical issues.
Your question was whether you should abandon nanostructure equilibration
because of this -- the answer is of course no.

Alex


On 6/30/2017 5:03 AM, Mohammad Roostaie wrote:

I asked it since I got some errors regarding the NPT equilibration,
also this link says that turn off the pressure coupling.

The errors which I received is as follow:

Fatal error:
The number of ranks you selected (14) contains a large prime factor 7.
In most cases this will lead to bad performance. Choose a number with
smaller prime factors or set the decomposition (option -dd) manually.
For more information and tips for troubleshooting, please check the
GROMACS
website at http://www.gromacs.org/Documentation/Errors
—---—

Halting parallel program mdrun_mpi on rank 0 out of 14
—
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 1.

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

Furthermore, I used -dd (with the values of 7 2 1) option, and I got
this error:

Fatal error:
1130 particles communicated to PME rank 14 are more than 2/3 times the
cut-off out of the domain decomposition cell of their charge group in
dimension y.
This usually means that your system is not well equilibrated.
For more information and tips for troubleshooting, please check the
GROMACS
website at Errors - Gromacs

Regards,
M


On Friday, June 30, 2017, 12:47:05 PM GMT+4:30, Alex
 wrote:


Is this a philosophical question? Yes, it is certainly possible for
graphene+peptide to exist in water under pressure.


On 6/30/2017 12:05 AM, Mohammad Roostaie wrote:

Hi All,
Is it possible and necessary to run NPT equilibration process on the

nanostructure systems (graphene+peptide in water)? Since I got some
errors regarding this process.

Regards,Mohammad



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Re: [gmx-users] Issue with the PDB generated after topology

[Mark Abraham]

Hi,

Your description is unclear - you seem to change whether a protein and a
chain are the same thing, or not. So I don't know what you think the
problem is :-)

Mark

On Sun, Jul 2, 2017 at 5:18 PM Khadija Amine  wrote:

> Dear Gromacs users,
>
> I'm running a protein complex simulations with the gromacs software.
>
> My complex is two different proteins named chain A (1-166 aa) and chain B
> (55-131)with 3 ions and one ligand.
>
> I have produced the topology for the every component of my complex using
> pdb2gmx program.
>
> However, when I have visualised the resulted pdb file with pymol, I can see
> the two displayed proteins but the amino acids sequence is not complete. I
> can see the chain A and not the chain B.
>
> Please, how can I fix this issue?
> Khadija
>
> *Khadija Amine*
> Ph.D. Biology and Health
> Biochemistry & Bioinformatics
> Phone: 9584
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[gmx-users] Simulation of an acetylated peptide covalently bound to a protein

[Zixian Li]

Hi Gromacs community,

I get stuck in a simulation of an acetylated peptide covalently bound to a
protein. Could someone please give me some insight?

My system consists of a short peptide bound to a protein. The peptide has 4
amino acids, with the N-terminal Val acetylated and the C-terminal Asp
bound to a Cys residue of a protein. A thioester bond is formed between the
backbone carboxyl group of Asp and the thiol group of Cys.

The scheme below shows the peptide-protein connection
(ACE-Val-Glu-Ile-Asp-CO---S-Cys...).

Protein: N-terminal-...-Ala162-Cys163-Arg164-...-C-terminal
.|..
...
S...
.
.|..
...
Peptide:..ACE-Val-Glu-Ile-N-C-C=O
..|.
...
.CH2
...
..I.
..
..O-C=O.
.

To simplify my system for test, I only kept Ala162, Cys163 and Arg164 the
three residues of the protein chain in addition to the bound peptide. I use
Gromacs version 4.6.2 with GROMOS 54A7 force field to do the simulation. I
copied the gromos54a7 folder from the topology library to my local working
directory and renamed it as gromos54a7_thioester. The specbond.dat file was
also copied to the local force field folder.

For the covalent linkage, I acquired the bonded parameters from Automated
Topology Builder (ATB) and Repository server. I submitted an all-atom
Asp-Cys dipeptide linked by thioester bond to ATB for bond length, angle
and dihedral parameters. In the ffbonded.itp file, I added the bond
parameters for the thioester linkage based on the ATB calculations.

;
#define gb_53   0.1780  5.9400e+06
;thioester bond S-C
;
#define ga_55   124.00  3074.03
;O1   C   SG
;
#define gd_46180.000  1.00  3
;CA  CB  SG  C

#define gd_47180.000  5.86  2
;CA  C   SG  CB
;
#define gd_48180.000  1.00  6
;N   CA  C   SG

I tried 2 ways to get the topology for the protein with a acetylated
peptide branch. Here are the problems I'm struggling with.

###
Way 1: Specify None for the peptide C-terminal with the hope for
establishing the linkage by specbond.dat file.

pdb2gmx -f Ala162-Cys163-Arg164_res300-ASP304.pdb -o CYS-ASP.gro -water spc
-ff gromos54a7_thioester -merge interactive -ter


Using the Gromos54a7_thioester force field in directory
./gromos54a7_thioester.ff

Opening force field file ./gromos54a7_thioester.ff/aminoacids.r2b
Reading Ala162-Cys163-Arg164_res300-ASP304_1p8A.pdb...
WARNING: all CONECT records are ignored
Read 58 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
Merge chain ending with residue ARG164 (chain id 'E', atom 22 NH2) and
chain starting with
residue ACE300 (chain id 'E', atom 24 CA) into a single moleculetype
(keeping termini)? [n/y]
y

Merged chains into joint molecule definitions at 1 places.

There are 1 chains and 0 blocks of water and 304 residues with 58 atoms

  chain  #res #atoms
  1 'E' 8 58

All occupancies are one
Opening force field file ./gromos54a7_thioester.ff/atomtypes.atp
Atomtype 1
Reading residue database... (gromos54a7_thioester)
Opening force field file ./gromos54a7_thioester.ff/aminoacids.rtp
Using default: not generating all possible dihedrals
Using default: excluding 3 bonded neighbors
Using default: generating 1,4 H--H interactions
Using default: removing proper dihedrals found on the same bond as a proper
dihedral
Residue 108
Sorting it all out...
Opening force field file ./gromos54a7_thioester.ff/aminoacids.hdb
Opening force field file ./gromos54a7_thioester.ff/aminoacids.n.tdb
Opening force field file ./gromos54a7_thioester.ff/aminoacids.c.tdb

Processing chain 1 'E' (58 atoms, 8 residues)
Identified residue ALA162 as a starting terminus.
Identified residue ARG164 as a ending terminus.
Identified residue ACE300 as a starting terminus.
Identified residue ASP304 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Select start terminus type for ALA-162
 0: NH3+
 1: NH2
 2: None
0
Start terminus ALA-162: NH3+
Select end terminus type for ARG-164
 0: COO-
 1: COOH
 2: None
0
End terminus ARG-164: COO-
Select start terminus type for ACE-300
 0: NH3+
 1: NH2
 2: None
2
Start terminus ACE-300: None
Select end terminus type for ASP-304
 0: COO-
 1: COOH
 2: None
2
End terminus ASP-304: None

---
Program pdb2gmx, VERSION 4.6.2
Source code file:
/home/zixian/Downloads/g

[gmx-users] Issue with the PDB generated after topology

[Khadija Amine]

Dear Gromacs users,

I'm running a protein complex simulations with the gromacs software.

My complex is two different proteins named chain A (1-166 aa) and chain B
(55-131)with 3 ions and one ligand.

I have produced the topology for the every component of my complex using
pdb2gmx program.

However, when I have visualised the resulted pdb file with pymol, I can see
the two displayed proteins but the amino acids sequence is not complete. I
can see the chain A and not the chain B.

Please, how can I fix this issue?
Khadija

*Khadija Amine*
Ph.D. Biology and Health
Biochemistry & Bioinformatics
Phone: 9584
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Re: [gmx-users] CGMD simulation is not running with antifreeze water beads and 20 fs timestep

[Sudip Das]

Hi Peter,

Sorry for the delay. According to your suggestion, I have equilibrated my
system with gradually increasing time step (1, 2, 5, 10, 15, 20 fs). After
that, the production step is running successfully.

Thanks a lot for your kind help!

Best regards,
Sudip

On Thu, Jun 29, 2017 at 2:32 PM, Peter Kroon  wrote:

> Hi Sudip,
>
>
> we had a short discussion over coffee. We also get these warnings, but
> they don't generally lead to significant instabilities. This means you
> probably have an equilibration issue. Could you try equilibrating your
> system with increasing timesteps? So first equilibrate with 5fs, then
> continue with 10 fs, 15fs and finally 20 fs.
>
> If that doesn't work, could you give a more detailed description of your
> system?
>
>
> Peter
>
>
> On 29-06-17 10:07, Peter Kroon wrote:
> > Hi Sudip,
> >
> >
> > there's a dedicated forum for these Martini questions on cgmartini.nl.
> > Recently there was a similar question there
> > (http://cgmartini.nl/index.php/component/kunena/7-mdp-
> options/5491-gpu-verlet-oscillational-period#7308).
> >
> > To summarize, the bonds between the backbone beads are extremely stiff.
> > If your protein is small/short enough you can change them to
> > constraints. I'll start a discussion in the group here on how to handle
> > it further.
> >
> >
> > Peter
> >
> >
> > On 29-06-17 09:06, Sudip Das wrote:
> >> Dear All,
> >>
> >> I am running a CGMD simulation of protein and surfactant in water with
> >> Martini2.0 force field for surfactant and water and ELNEDYN2.2 force
> field
> >> for protein.
> >>
> >> The system is running fine with 20 fs integration timestep. But it
> leads to
> >> solid phase of water. So, I have introduce antifreeze water beads (which
> >> are 10% in number w.r.t. the total number of water beads). But after
> this,
> >> simulation is not at all running with 20 fs timestep and gives the
> error:
> >>
> >> segmentation fault (signal 11)
> >>
> >> Within output file, it shows:
> >>
> >> Step 2, time 0.04 (ps)  LINCS WARNING
> >> relative constraint deviation after LINCS:
> >> rms 0.007237, max 0.028381 (between atoms 20 and 21)
> >> bonds that rotated more than 30 degrees:
> >>  atom 1 atom 2  angle  previous, current, constraint length
> >>  20 21   30.40.1981   0.1895  0.1950
> >>
> >>
> >> I have tried to solve it in several ways, i.e., decreasing the time
> steps
> >> (it is running fine with 2 fs), equilibrating the system properly,
> >> compiling and running in serial version of gromacs (to test whether the
> >> error comes due to domain decomposition during parallel run) etc. Even
> >> though, I am getting the same error.
> >>
> >> While compiling the job with grompp, I got the below warning:
> >>
> >> WARNING 1 [file system.top, line 18]:
> >>   The bond in molecule-type Protein_A between atoms 1 BB and 2 BB has an
> >>   estimated oscillational period of 9.7e-02 ps, which is less than 5
> times
> >>   the time step of 2.0e-02 ps.
> >>   Maybe you forgot to change the constraints mdp option.
> >>
> >> But, following the link
> >> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-
> users/2014-May/089120.html
> >> , I have ignored this warning using -maxwarn flag. Probably this
> wouldn't
> >> be the cause for this error, as I got exactly the same warning for the
> >> system without antifreeze water beads.
> >>
> >>
> >> Please help me to solve this problem. I would be happy to share my
> files if
> >> needed.
> >>
> >> Thanks in advance!
> >>
> >> Best regards.
> >> Sudip
> >
>
>
>
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Re: [gmx-users] Checkpoint files error

[Mark Abraham]

Hi,

Use grompp -t state.cpt to do an exact continuation while changing the tpr
settings. As you saw, mdrun -cpi expects things to stay the same. The gro
file has lower precision, so should be used for visualization convenience
only.

Mark

On Sat, 1 Jul 2017 19:12 Apramita Chand  wrote:

> Dear All,
> After equilibration, I want to pass on the checkpoint files state.cpt  for
> production run for which I give the command
> g_mdrun -s md.tpr -c md.gro -o md.trr -cpi state.cpt -cpo state_md.cpt
>
> The job terminates with error that output files for checkpoint files are
> insufficient
> Just 1 out of 3files are present
> Required: npt.trr ,npt.edr
>
> I have the above mentioned files in the folder ,still the error message
> exists
>
> What is the correct procedure to pass checkpoint files?
> Also,for generation of tpr file,we use .gro files from the last run.what
> are the advantages of using .cpt files? Are they essential?
>
> Thanks in advance for your suggestions
>
> Yours sincerely
> Apramita
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