[gmx-users] Can't read xxx bytes of pullf.xvg to compute checksum

[Diez Fernandez, Amanda]

Dear users,

I am running many (almost identical) simulations and every so often one crashes 
and I get this message. Initially I just deleted everything, started from 
scratch and the problem was solved. However it is starting to be annoying.

Any idea what is happening?

Is it an error of Gromacs or the supercomputer?

Thanks.



Fatal error:

Can't read 158727 bytes of 'pullf.xvg' to compute checksum. The file has been 
replaced or its contents have been modified. Cannot do appending because of 
this condition.

For more information and tips for troubleshooting, please check the GROMACS

website at http://www.gromacs.org/Documentation/Errors
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Re: [gmx-users] Anybody using Silica InterfaceFF on Gromacs?

[Diez Fernandez, Amanda]

Hi Mark, 

*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?

This is the extract from the supporting information of the paper I refer
to that explains the issue
(³http://irep.ntu.ac.uk/id/eprint/4652/7/4652__Perry_SI.pdf²):
"Full inclusion of attractive nonbond interactions between 1,4 bonded
atoms in most force fields (CHARMM, CVFF, PCFF, COMPASS) requires a 4%
increase in r (the equilibrium bond length parameter of the forcefield)
Partial inclusion of attractive nonbond interactions between 1,4 bonded
atoms (50% of Lennard-Jones interactions and 5/6 of Coulomb interactions
in AMBER) requires only a 2.5% increase, and 12-6 LJ parameters identical
to these in CVFF and CHARMM can then be used."

My particular issue was that I assumed gen-pairs=yes in the [ default ]
section of the topology file meant that Gromacs automatically generated a
list of atoms undergoing 1-4 interactions (as well as automatically
generating the modified LJ and Coulomb parameters for those interactions).
When I proceeded to manually specify the list of atoms undergoing 1-4
interactions within the [pairs] section of the topology, the silica system
compressed during the simulation to produce the correct equilibrium bond
length observed experimentally.

Thanks, 
Amanda  





On 03/07/2017, 06:34, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se
on behalf of gromacs.org_gmx-users-requ...@maillist.sys.kth.se"
 wrote:

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>
>Today's Topics:
>
>   1. Re: Anybody using Silica InterfaceFF on Gromacs? (Mark Abraham)
>   2. Re: Can not open file: run.trr (Mark Abraham)
>   3. Re: Can not open file: run.trr (Mark Abraham)
>   4. Re: Anybody using Silica InterfaceFF on Gromacs? (Alex)
>   5. Multiple output log. xtc .edr files generated using  mpirun
>  (Abhishek Acharya)
>   6. Grid Spacing (Apramita Chand)
>
>
>--
>
>Message: 1
>Date: Mon, 03 Jul 2017 00:03:52 +
>From: Mark Abraham 
>To: gmx-us...@gromacs.org
>Subject: Re: [gmx-users] Anybody using Silica InterfaceFF on Gromacs?
>Message-ID:
>   
>Content-Type: text/plain; charset="UTF-8"
>
>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
>> --
>> Gromacs Users mailing list
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>> * Please search the archive at
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>> posting!
>>
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>> send a mail to gmx-users-requ...@gromacs.org.
>>
>
>
>--
>
>Message: 2
>Date: Mon, 03 Jul 2017 00:06:16 +
>From: Mark Abraham 
>To: gmx-us...@gromacs.org, gromacs.org_gmx-users@maillist.sys.kth.se
>Subject: Re: [gmx-users] Can not open 

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
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>
>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
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>> * Please search the archive at
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>> posting!
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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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>>
>
>
>--
>
>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

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 158, Issue 181

[Diez Fernandez, Amanda]

Hi, 
Thanks Alex. 
I have now solved the problem.
I assumed ³gen - pairs = yes² within [ Defaults ] of the topology was
generating automatically a list of pairs of 1-4 interactions as well as
modifying the LJ and QQ parameters for those interactions.
I have now listed the 1-4 pairs within [ Pairs ] and it has led to the
correct equilibrium bond length.
Cheers, 
Amanda

On 28/06/2017, 19:22, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se
on behalf of gromacs.org_gmx-users-requ...@maillist.sys.kth.se"
<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
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>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
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>
>
>Today's Topics:
>
>   1. Re: Atom types comparison between CGenFF and Charm36FF
>  (Justin Lemkul)
>   2. Re: Atom types comparison between CGenFF and Charm36FF
>  (Mohsen Ramezanpour)
>   3. Re: Using SLLOD to find Viscosity (nishi kashyap)
>   4. Deform a liquid (nishi kashyap)
>   5. Anybody using Silica InterfaceFF on Gromacs?
>  (Diez Fernandez, Amanda)
>   6. Re: Anybody using Silica InterfaceFF on Gromacs? (Alex)
>
>
>--
>
>Message: 1
>Date: Wed, 28 Jun 2017 10:21:32 -0600
>From: Justin Lemkul <jalem...@vt.edu>
>To: gmx-us...@gromacs.org
>Subject: Re: [gmx-users] Atom types comparison between CGenFF and
>   Charm36FF
>Message-ID: <350dd743-bdfa-76ee-a401-039cadaf1...@vt.edu>
>Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
>On 6/28/17 9:10 AM, Mohsen Ramezanpour wrote:
>> Thanks Justin for your comment.
>> 
>> I have a bit of difficulty for the finding the analog parts to these two
>> parts.
>> 
>> Is there any database (preferably with shapes) for the molecules
>>available
>> in charmmFF?
>> 
>
>The CHARMM topology files have full residue names and chemical structure
>drawings.  Within the toppar directory (download the tarball from our
>site), 
>just grep -r "RESI" *
>
>If you have additional questions about this or CHARMM parametrization,
>contact 
>me off list as this is not really a GROMACS issue.
>
>-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
>
>==
>
>
>--
>
>Message: 2
>Date: Wed, 28 Jun 2017 10:38:13 -0600
>From: Mohsen Ramezanpour <ramezanpour.moh...@gmail.com>
>To: Discussion list for GROMACS users <gmx-us...@gromacs.org>
>Subject: Re: [gmx-users] Atom types comparison between CGenFF and
>   Charm36FF
>Message-ID:
>   

[gmx-users] Anybody using Silica InterfaceFF on Gromacs?

[Diez Fernandez, Amanda]

Hi,
I converted the InterfaceFF silica parameters to use in Gromacs (and to be 
compatible with the AMBER forcefield) and have gotten some problems, namely I 
am getting a slightly bigger equilibrium bond length than I should.
I was wondering if there were other Gromacs users out there that have used 
InterfaceFF silica parameters in Gromacs.

Many thanks,
Amanda
-- 
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Re: [gmx-users] Difference between output_coordinates.gro and trajectory.xtc coordinates

[Diez Fernandez, Amanda]

Hi Mark, 

Thanks.

>mdrun will generally "make molecules whole" for -c, but otherwise doesn't
>care. Implementing general triclininc 3D periodicity with domain
>decomposition is a messy business.
 
I am not using a triclinic unit cell (all angles are 90 in the input .pdb
file). Wouldn¹t the output also be represented in a cuboid unit cell?
For this case ³making the molecule whole² is an arbitrary decision as it
is an infinite substrate.
Is this discrepancy something I should worry about, or is it just a
question of visualisation?
 
I am getting a warning  ³xx inconsistent shifts check your topology². I
can¹t spot anything obvious and I do have periodic-molecules=yes in
file.mdp. 

Thanks!
Amanda
 






On 22/06/2017, 12:27, "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
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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: Simulation of Carbon nanotube (Nikhil Maroli)
>   2. Re: Regarding the charge of the atom in the .rtp file
>  (Mark Abraham)
>   3. Re: Difference between output_coordinates.gro and
>  trajectory.xtc coordinates (Mark Abraham)
>   4. Re: Difference between output_coordinates.gro and
>  trajectory.xtc coordinates (Mark Abraham)
>   5. Re: positive potential energy (Mark Abraham)
>   6. Re: positive potential energy (Mark Abraham)
>
>
>--
>
>Message: 1
>Date: Thu, 22 Jun 2017 16:29:49 +0530
>From: Nikhil Maroli 
>To: gromacs.org_gmx-users@maillist.sys.kth.se
>Subject: Re: [gmx-users] Simulation of Carbon nanotube
>Message-ID:
>   
>Content-Type: text/plain; charset="UTF-8"
>
>Dear Justin,
>I have generated topology for CNT using gmx x2top. There is cyclic peptide
>nanotube wrapped over the CNT (eight CP rings in equal intervals)
>otherwise
>let's say, CNT is inserted into the Cyclic peptide nanotube. I wanted to
>put the whole system into the lipid bilayer. I was using charmm-gui for
>the
>input generator since it provides easy hand on CPN, So is it possible to
>convert the CNT topology which generated with gmx x2top to 'Topology and
>Parameters' for charmm-gui (*.rtf and *.prm)?
>Thanks in advance.
>
>
>--
>
>Message: 2
>Date: Thu, 22 Jun 2017 11:08:45 +
>From: Mark Abraham 
>To: gmx-us...@gromacs.org
>Subject: Re: [gmx-users] Regarding the charge of the atom in the .rtp
>   file
>Message-ID:
>   

Re: [gmx-users] Difference between output_coordinates.gro and trajectory.xtc coordinates

[Diez Fernandez, Amanda]

Hi Mark, 
Thank you for your reply.

It is exactly the opposite though: for output_coordinates.gro which is the
output from:

 mdrun Š -c output_coordinates.gro

it seems like atoms are diffusing out of the box.

In the trajectory, I allow atoms to be seen to diffuse out of the box,
using -pbc nojump, and I don¹t see them diffuse out (They stay within the
unit cell, which is what I expect being a silica substrate at room
temperature over a very short period of time).

So what puzzles me is why for the output of (mdrun -c) the atoms seem to
diffuse out, specially so if I cannot see this in the trajectory.

Sorry if I didn¹t explain it very clearly last time.

Thanks!

On 22/06/2017, 06:18, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se
on behalf of gromacs.org_gmx-users-requ...@maillist.sys.kth.se"
<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
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>or, via email, send a message with subject or body 'help' to
>   gromacs.org_gmx-users-requ...@maillist.sys.kth.se
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>You can reach the person managing the list at
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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: Difference between output_coordinates.gro and
>  trajectory.xtc coordinates (Mark Abraham)
>   2. Re: (no subject) (Mark Abraham)
>   3. Re: puzzled by unexpected [ bonds ] section resulting from
>  running gmx x2top (Jose Borreguero)
>   4. Re: GROMACS and SIMtoEXP (Sanim Rahman)
>   5. Re: Regarding the charge of the atom in the .rtp file (Dilip H N)
>
>
>--
>
>Message: 1
>Date: Wed, 21 Jun 2017 17:29:53 +
>From: Mark Abraham <mark.j.abra...@gmail.com>
>To: gmx-us...@gromacs.org
>Subject: Re: [gmx-users] Difference between output_coordinates.gro and
>   trajectory.xtc coordinates
>Message-ID:
>   <camnumarks3ogwr-gbht9gotmwburcobrbkjc1es+oy-c2ep...@mail.gmail.com>
>Content-Type: text/plain; charset="UTF-8"
>
>Hi,
>
>On Wed, Jun 21, 2017 at 6:49 PM Diez Fernandez, Amanda <
>amanda.die...@imperial.ac.uk> wrote:
>
>> Hi Justin,
>> Thank you for your reply.
>>
>> Here are the links to the images of:
>> -the output coordinates
>> -and last frame of trajectory.
>>
>> Output coordinates which look wrong:
>> 
>>http://i1036.photobucket.com/albums/a443/amanda222lld/output_coordinates_
>>zp
>> stuqkgjd2.png
>> 
>><http://i1036.photobucket.com/albums/a443/amanda222lld/output_coordinates
>>_zpstuqkgjd2.png>
>>
>> Last frame from trajectory which looks OK:
>> 
>>http://i1036.photobucket.com/albums/a443/amanda222lld/last_frame_traj_zps
>>n2
>> 7nzusn.png
>> 
>><http://i1036.photobucket.com/albums/a443/amanda222lld/last_frame_traj_zp
>>sn27nzusn.png>
>>
>> For the last frame of the trajectory I used trjconv -pbc nojump to make
>> sure the atoms were not being wrapped around the box.
>
>
>That's what you're getting. See "gmx help trjconv" where it specifically
>says that "-pbc nojump" will lead to atoms appearing to diffuse out of the
>box.
>
>It seems like you want trjconv -pbc atom, so all the atoms are in the same
>box. That won't necessarily match what mdrun -c writes, either, because
>that is not something for which we have designed. There's an infinite
>number of equivalent representations of any system, and a large number of
>plausible representations that someone might want to use for different
>purposes, so we've left the choice to you, with the tools and
>documentation
>to get something that makes you happy :-)
>
>Mark
>
>
>--
>
>Message: 2
>Date: Wed, 21 Jun 2017 17:35:04 +
>From: Mark Abraham <mark.j.abra...@gmail.com>
>To: gmx-us...@gromacs.org
>Subject: Re: [gmx-users] (no subject)
>Message-ID:
>   <camnumaqmhqcktt0u_nbka6lks+jsa53udgpvmtpvc_qcvuc...@mail.gmail.com>
>Content-Type: text/plain; charset="UTF-8"
>
>Hi,
>
>On Wed, Jun 21, 2017 at 4:32 PM Shivangi Agarwal <
>shivangi.agarwal...@gmail.com> wrote:
>
>> Hi
>> But it is broken. ..
>>
>
>Nope, it's just in one of the infinite number of equivalent
>representations
>

Re: [gmx-users] Difference between output_coordinates.gro and trajectory.xtc coordinates

[Diez Fernandez, Amanda]

zed all OK, however, mdrun produced a counfout.gro
>file that no longer contains the Na Cl ions added to the system. When
>setting up the simulation, the input confout.gro has no Na Cl ions, and
>the procedure is therefore not working.
>
>Why is this so? Does one have to do the genion procedure each time one
>wants to use gromp with a new mdp file?
>
>Sergio Manzetti 
>
>[ http://www.fjordforsk.no/logo_hr2.jpg ]
>
>[ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/
>|   ] 
>Midtun 
>6894 Vangsnes 
>Norge 
>Org.nr. 911 659 654
>Tlf: +47 57695621 
>[ http://www.oekolab.com/ | ?kolab? ] | [ http://www.nanofact.no/ |
>Nanofactory? ] | [ http://www.aq-lab.no/ | AQ-Lab? ] | [
>http://www.phap.no/ | FAP ]
>
>
>
>--
>
>Message: 3
>Date: Wed, 21 Jun 2017 16:39:40 +0200
>From: gozde ergin <gozdeeer...@gmail.com>
>To: gmx-us...@gromacs.org
>Subject: Re: [gmx-users] non-bonded sigma for amino
>   nitrogen?carboxylate oxygen interactions in OPLSAA in GROMACS
>Message-ID: <03f1d960-7f47-4921-90de-cbfeefb32...@gmail.com>
>Content-Type: text/plain; charset=utf-8
>
>Hi MArk,
>
>Thanks for the respond. I understood that point however I still do not
>get which sigma to change.
>I the paper JCTC 2017, Miller et. al. they have mentioned that they
>increase the for nitrogen?carboxylate oxygen interactions in OPLSAA.
>However there are two sigma in oplsaa.ff/ffnonbonded.itp one for amino
>notrogen and one for carboxylate oxygen.
>
>  
>sigmaepsilon
> opls_287   N3   7  14.00670-0.300   A3.25000e-01  7.11280e-01
> opls_272   O2   8  15.99940-0.800   A2.96000e-01  8.78640e-01
>
>Which one defines the amino nitrogen?carboxylate oxygen interactions?
>Which sigma should I change?
>
>Thanks
>> On 21 Jun 2017, at 16:21, Mark Abraham <mark.j.abra...@gmail.com> wrote:
>> 
>> Hi,
>> 
>> Different force fields work differently and thus are implemented
>> differently. Look at oplsaa.ff/ffnonbonded.itp and you will see that
>>sigma
>> is a property of the atomtype
>> 
>> Mark
>> 
>> On Wed, Jun 21, 2017 at 4:16 PM gozde ergin <gozdeeer...@gmail.com>
>>wrote:
>> 
>>> Dear users,
>>> 
>>> I am trying to change the sigma value of amino nitrogen?carboxylate
>>>oxygen
>>> interactions in OPLSAA in GROMACS.
>>> However I have difficulties to understand which parameter i should
>>>change
>>> in ffnonbonded.itp file?
>>> I am looking something like [ nonbond_params ] section however it is
>>>not
>>> exist in ffnonbonded.itp?
>>> Any help would be appreciated.
>>> 
>>> Thanks in advance.
>>> --
>>> Gromacs Users mailing list
>>> 
>>> * Please search the archive at
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>>> posting!
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>>posting!
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>
>
>
>--
>
>Message: 4
>Date: Wed, 21 Jun 2017 10:42:42 -0400
>From: Justin Lemkul <jalem...@vt.edu>
>To: gmx-us...@gromacs.org
>Subject: Re: [gmx-users] Difference between output_coordinates.gro and
>   trajectory.xtc coordinates
>Message-ID: <563e25e1-a01a-ad3b-94c6-6d0962acd...@vt.edu>
>Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
>On 6/21/17 7:11 AM, Diez Fernandez, Amanda wrote:
>> Hi all,
>> I am running a simulation and I find that the output coordinates of the
>>simulation stored in ?final_coordinates.gro? are distinctively different
>>to any of the frames from ?trajectory.gro? which I obtain from :
>> 
>> trjconv ?s file.tpr ?f trajectory.xtc ?o trajectory.gro
>> 
>> When I visualise final_coordinates.gro they look wrong, when I
>>visualise trajectory.gro frame by frame it looks correct.
>> 
>> How can this be possible? Is it a commo

[gmx-users] Difference between output_coordinates.gro and trajectory.xtc coordinates

[Diez Fernandez, Amanda]

Hi all,
I am running a simulation and I find that the output coordinates of the 
simulation stored in “final_coordinates.gro” are distinctively different to any 
of the frames from “trajectory.gro” which I obtain from :

trjconv –s file.tpr –f trajectory.xtc –o trajectory.gro

When I visualise final_coordinates.gro they look wrong, when I visualise 
trajectory.gro frame by frame it looks correct.

How can this be possible? Is it a common problem?

Thank you,

Amanda
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[gmx-users] xx inconsistent shift check your topology

[Diez Fernandez, Amanda]

Dear Gromacs users,
I am simulating a silica slab and get a warning stating there are “xx 
inconsistent shifts, check topology”.
In my .mdp file I already have periodic-molecules=yes.
Is this a common error? Do you recommend any approach to finding what causes it?

Thank you,
Amanda
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[gmx-users] NVE Temperature Drop ONLY When Applying Restraints

[Diez Fernandez, Amanda]

Dear Users,
I was observing significant temperature drops in my system when switching from 
NPT equilibration to NVE.
Within 1ns of the NVE run the temperature was so low the water was freezing.
Trying to understand what was causing it, I have observed that it only occurs 
when I apply position restraints to certain water molecules (which I need to do 
for my final simulation).
Without any restraints the temperature does not drop.
I was wondering why this was happening.
Excuses in advance is this has already been discussed or has been explained 
elsewhere.

Many thanks,
Amanda
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Re: [gmx-users] Diffusion coefficient water

[Diez Fernandez, Amanda]

Thanks Justin and Nikhil,

1) So in principle is it expected that results will be different and I
should take my final value to be the average of, say, 10 simulations?

2)If so, the average over my simulations is not similar to the published
average. They also use a unit cell of 216 molecules (I use 221 molecules).
They have "long-range corrections for both the energy and pressure². Is
this equivalent to DispCorr= EnerPres ? What other
corrections should I do?

Thanks,
Amanda
 
 


On 17/08/2016, 19:28, "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
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>
>
>Today's Topics:
>
>   1. Re: Diffusion coefficient water (Nikhil Maroli)
>   2. Re: Diffusion coefficient water (Justin Lemkul)
>   3. is there martini CG parameters for K+ ion? (li he)
>   4. Re: Diffusion coefficient water (li he)
>   5. Fwd: is there martini CG parameters for K+ ion? (li he)
>   6. Re: Diffusion coefficient water (li he)
>
>
>--
>
>Message: 1
>Date: Wed, 17 Aug 2016 21:49:45 +0530
>From: Nikhil Maroli 
>To: gromacs.org_gmx-users@maillist.sys.kth.se
>Subject: Re: [gmx-users] Diffusion coefficient water
>Message-ID:
>   

[gmx-users] Diffusion coefficient water

[Diez Fernandez, Amanda]

Dear Gromacs users,

I was trying to reproduce the published values for the diffusion coefficient of 
SPCFw water (2.3 +/- 0.08 x 10^-9 m^2/s  )before using it in some of my 
simulations and I am failing to do so.
More worryingly I get different results for different identical runs.
I am using a 2nm side cubic cell containing 221 water molecules and a time step 
of 0.5fs (larger timestep results in a warning since I am not applying any 
constraints).
I ran 6 identical simulations (only difference is the random initial 
velocities) and I got these different values and error magnitudes.
The trajectories are 10ns long. I discarded the first 2ns for the msd 
calculation.

 Nth Simulation Diffusion Coefficient (x 10^-9 m^2/s)

1  2.95  +/-  0.071
2  2.71  +/-  0.158
3  2.52  +/-   0.007
4  2.96   +/-   0.26
5  2.62   +/-  0.07
6  2.71  +/-  0.158

Is it normal that I get different results like this?  (Despite averaging over 
more than 7ns and 221 molecules?).

Many thanks in advance.  Below are the detailed parameters.

Amanda

Detailed parameters:

nstlist = 10

ns_type = grid

rlist   = 0.9

coulombtype = PME

rcoulomb= 0.9

fourierspacing  = 0.12

pme_order   = 4

ewald_rtol  = 1e-6

vdw-type= cut-off

rvdw= 0.9

pbc = xyz

tcoupl  = nose-hoover

tc_grps = SYSTEM

tau_t   = 0.4

ref_t   = 298

nsttcouple  =-1

nh-chain-length = 1

pcoupl  = Berendsen

pcoupltype  = isotropic

tau_p   = 10.0

compressibility = 4.5e-5

ref_p   = 1.01325

refcoord-scaling= all

DispCorr= EnerPres

gen_vel = yes

gen_temp= 293

gen_seed= -1

constraints = none
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Re: [gmx-users] Segmentation Fault - Water on Substrate

[Diez Fernandez, Amanda]

Hi Mark, 
Thanks for your quick response.

In the all three minimisation.mdp files (the one for water.pdb,
substrate.pdb and merged.pdb) I have:

pbc = xyz

To minimise the water.pdb file I have:

periodic_molecules = no ;


To minimise the substrate.pdb and then the merged.pdb I have:

periodic_molecules = yes ;


Is this what you meant?
When I minimise substrate.pdb or water.pdb alone it works. When I combine
them and minimise merged.pdb it doesn¹t.

Cheers,
Amanda



>--
>
>Message: 5
>Date: Sun, 26 Jun 2016 09:53:46 +
>From: Mark Abraham <mark.j.abra...@gmail.com>
>To: gmx-us...@gromacs.org, "gromacs.org_gmx-users@maillist.sys.kth.se"
>   <gromacs.org_gmx-users@maillist.sys.kth.se>
>Subject: Re: [gmx-users] Segmentation Fault - Water on Substrate
>Message-ID:
>   <camnumat12f5adcfp8rq3cvft21vyveqkbdt0lykrnwwlgrg...@mail.gmail.com>
>Content-Type: text/plain; charset=UTF-8
>
>Hi,
>
>You're presumably making one of your formerly periodic dimensions
>differently periodic when you combine your boxes. If your input structure
>has molecules with coordinates that are broken across the former boundary,
>you need to make them whole before your merge can work sanely.
>
>Mark
>
>On Sun, Jun 26, 2016 at 11:45 AM Diez Fernandez, Amanda <
>amanda.die...@imperial.ac.uk> wrote:
>
>> Dear Gromacs users,
>>
>> I am want to simulate water on a  substrate.
>> I have a water.pdb file with the coordinates of a cuboid of water and a
>> substrate.pdb file with the coordinates of the substrate. The box
>> dimensions along the x and y directions are identical for both  files.
>> I run two simulations to minimise both structures separately. I get no
>> error, meaning the topology file must be correct (is this a correct
>> assumption?) This also ensures that all atoms in the minimised.pdb files
>> are within the box I have specified  (as opposed to before, when some
>>atoms
>> were slightly outside).
>> I then have a script to merge both minimised .pdb files.
>> I minimise the system and get a segmentation fault:
>>
>> 40783 Segmentation fault
>>
>> Further, in the file.log I get:
>>
>>
>> Steepest Descents:
>>
>>Tolerance (Fmax)   =  6.0e+01
>>
>>Number of steps=   10
>>
>>Step   Time Lambda
>>
>>   00.00.0
>>
>>
>>Energies (kJ/mol)
>>
>>Bond  Angle  LJ-14 Coulomb-14LJ
>>(SR)
>>
>> 1.36501e+046.58753e+044.22206e+04   -1.70332e+06
>>-nan
>>
>>Coulomb (SR)   Coul. recip.  Potential Pressure (bar)
>>
>> 1.18196e+062.65781e+03   -nan   -nan
>>
>>
>>
>> I have visualised the input merged.pdb file and have also checked the
>> minimum and maximum coordinates of water and substrate and I am sure
>>there
>> is no atom overlap. In fact, water and substrate atoms are separate by
>>more
>> than 3A.  ( I have also tried previously with smaller separations).
>>
>> What could else could I check?
>>
>> Thanks,
>> Amanda
>> --
>> 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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>> send a mail to gmx-users-requ...@gromacs.org.
>>
>
>
>--
>
>Message: 6
>Date: Sun, 26 Jun 2016 09:53:46 +
>From: Mark Abraham <mark.j.abra...@gmail.com>
>To: gmx-us...@gromacs.org, "gromacs.org_gmx-users@maillist.sys.kth.se"
>   <gromacs.org_gmx-users@maillist.sys.kth.se>
>Subject: Re: [gmx-users] Segmentation Fault - Water on Substrate
>Message-ID:
>   <camnumat12f5adcfp8rq3cvft21vyveqkbdt0lykrnwwlgrg...@mail.gmail.com>
>Content-Type: text/plain; charset=UTF-8
>
>Hi,
>
>You're presumably making one of your formerly periodic dimensions
>differently periodic when you combine your boxes. If your input structure
>has molecules with coordinates that are broken across the former boundary,
>you need to make them whole before your merge can work sanely.
>
>Mark
>
>On Sun, Jun 26, 2016 at 11:45 AM Diez Fernandez, Amanda <
>amanda.die...@imperial.ac.uk> wrote:
>
>> Dear Gromacs users,
>>
>> 

[gmx-users] Segmentation Fault - Water on Substrate

[Diez Fernandez, Amanda]

Dear Gromacs users,

I am want to simulate water on a  substrate.
I have a water.pdb file with the coordinates of a cuboid of water and a 
substrate.pdb file with the coordinates of the substrate. The box dimensions 
along the x and y directions are identical for both  files.
I run two simulations to minimise both structures separately. I get no error, 
meaning the topology file must be correct (is this a correct assumption?) This 
also ensures that all atoms in the minimised.pdb files are within the box I 
have specified  (as opposed to before, when some atoms were slightly outside).
I then have a script to merge both minimised .pdb files.
I minimise the system and get a segmentation fault:

40783 Segmentation fault

Further, in the file.log I get:


Steepest Descents:

   Tolerance (Fmax)   =  6.0e+01

   Number of steps=   10

   Step   Time Lambda

  00.00.0


   Energies (kJ/mol)

   Bond  Angle  LJ-14 Coulomb-14LJ (SR)

1.36501e+046.58753e+044.22206e+04   -1.70332e+06   -nan

   Coulomb (SR)   Coul. recip.  Potential Pressure (bar)

1.18196e+062.65781e+03   -nan   -nan



I have visualised the input merged.pdb file and have also checked the minimum 
and maximum coordinates of water and substrate and I am sure there is no atom 
overlap. In fact, water and substrate atoms are separate by more than 3A.  ( I 
have also tried previously with smaller separations).

What could else could I check?

Thanks,
Amanda
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[gmx-users] md of only water - obtaining different pressure in the x , y and z directions

[Diez Fernandez, Amanda]

Hi,

I am running a simulation which contains only water (using the spc216.gro 
coordinates and TIP3P model) in an NPT ensemble.
 I get different values for the average pressure in the x y and z directions.
I am running the simulation for up to 10s in a 4nm side cube unit cell.
I am using a Nose Hoover thermostat and a Parrinello-Rahman barostat applied 
isotropically, with target pressure 1 bar.

The averages after 1ns are:


Energy  Average   Err.Est.   RMSD  Tot-Drift

---

Temperature 299.9990.000986.07906 0.00504098  (K)

Pressure 1.3174  0.066350.061   -0.14372  (bar)

Box-X4.03960.00013 0.00874048 -5.7234e-06  (nm)

Box-Y4.03960.00013 0.00874048 -5.7234e-06  (nm)

Box-Z4.03960.00013 0.00874048 -5.7234e-06  (nm)

Pres-XX 1.11668  2 485.28   0.288761  (bar)

Pres-YY   -0.762405  1427.866-6.2632  (bar)

Pres-ZZ 3.597922.4410.5465.54328  (bar)


The averages over the 10 ns are :


Energy  Average   Err.Est.   RMSD  Tot-Drift

---

Temperature 300  8e-054.00951 0.000535848  (K)

Pressure1.22566 0.0067275.993 -0.0289005  (bar)

Box-X   4.039295.1e-05 0.00823878 0.000126042  (nm)

Box-Y   4.039295.1e-05 0.00823878 0.000126042  (nm)

Box-Z   4.039295.1e-05 0.00823878 0.000126042  (nm)

Pres-XX 1.29387   0.73385.989  0.0898956  (bar)

Pres-YY 1.35691   0.74378.8413.13618  (bar)

Pres-ZZ 1.02621   0.84377.022   -3.31278  (bar)



Why is the average pressure in the in each direction different?

And why is the drift of the XX direction so much lower than in the YY and ZZ 
directions?


Many thanks!

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