[gmx-users] is there a way to get pullx.xvg and pullf.xvg from traj_comp.xtc?

[Ming Tang]

Dear list,

I did SMD, but saved the pullx.xvg and pullf.xvg much less frequently compared 
to the traj_comp.xtc. is it possible to get a more frequently written pull COM 
coordinates and forces based on the traj_compxtc file I have?

Thank you,
Ming
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[gmx-users] is there a way to get pullx.xvg and pullf.xvg from traj_comp.xtc?

[Ming Tang]

Dear list,

I did SMD, but saved the pullx.xvg and pullf.xvg much less frequently compared 
to the traj_comp.xtc. is it possible to get a more frequently written pull COM 
coordinates and forces based on the traj_compxtc file I have?

Thank you

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Re: [gmx-users] how to distance between COM of two groups of atoms?

[Ming Tang]

Fixed!
Thanks.
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[gmx-users] Water molecule can not be settled

[Billy Williams-Noonan]

Hi Mark,

Late response.  I meant reducing the emstep parameter.  I've found this
helps with minimising water molecules that are too close together.  That or
you could manually shift the relevant waters and re-minimise. Apologies for
the typo.  Looks like the problem is sorted now.

Billy

On 1 July 2016 at 02:22, Mark Abraham > wrote:

> Hi,
>
> Run with one rank, e.g. gmx mdrun -ntmpi 1
>
> Mark
>
> On Thu, Jun 30, 2016 at 6:11 PM zeineb SI CHAIB  >
> wrote:
>
> > Dear Mark,
> >
> > Thank you for your orientation. I looked in Google and based on what you
> > advised me, I prepared the following mdp file
> >
> > integrator = steep
> > nsteps = 1000
> > emtol = 1000.0
> > emstep = 0.01
> > energygrps= system
> >
> > pbc = no
> > nstlist = 0
> > ns-type = simple
> > rlist   = 0
> >
> > cutoff-scheme = group
> > coulombtype  = cut-off
> > rcoulomb = 0
> > vdw-type = Cut-off
> > rvdw = 0
> >
> >
> > However, I'm working with GROMACS 5.1.2 and apparently some combinaisons
> > doesn't work. When I run EM with these mdp parameters I got the following
> > error:
> >
> > Fatal error:
> > Domain decomposition does not support simple neighbour searching, use
> grid
> > searching or run with one MPI rank
> >
> > Is there a problem with these parameters?
> >
> > Zeineb
> >
> > --
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-- 
Billy Noonan*|*PhD Student*|*Bsci ( *Adv* ), IA Hon

*LinkedIn Profile

**|*   +61420 382 557

Monash Institute for Pharmaceutical Sciences ( *MIPS* )
Royal Parade, Parkville, 3052



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Re: [gmx-users] md with multiple ligands

[Billy Williams-Noonan]

Hi Justin,

I've found that I get this error with my relative FEP calculations if my
.gro file with the relevant protein and ligand coordinates, describes the
protein numbering from a1-3017, and the ligand from 3018 onwards for
example, while in my topology file, a1-3017 refer to the same protein, and
afterwards I start label the first atom of my ligand as 1 again, instead of
3018.

This problem usually pops up when I manually combine the relevant protein
and ligand molecule type and make an error with the numbering.

Kind regards,

Billy

On Friday, 1 July 2016, Justin Lemkul  wrote:

>
>
> On 6/30/16 11:22 PM, Billy Williams-Noonan wrote:
>
>> Hi Thanh,
>>
>> Maybe try to check if the numbering of your atoms in the topology files is
>> consistent with the .pdb or .gro files they describe.
>>
>>
> Coordinate file and topology file numbering are different and use
> different conventions.  In fact, if one numbers a topology using global
> atom numbers from a coordinate file, it is what causes the error the OP
> reports.  Each [moleculetype] directive must be numbered consecutively from
> 1; after that, the only match with the coordinate file is based on the
> correct appearance of atom names (thus a link between [molecules] in the
> .top and the coordinates themselves).
>
> -Justin
>
> Billy
>>
>> On 1 July 2016 at 09:20, Thanh Le  wrote:
>>
>>
>>> On Jun 30, 2016, at 3:48 PM, Thanh Le  wrote:

 My name is Thanh Le, a graduate student in chemistry. Currently, I am

>>> using gromacs to do a dynamics simulation for my RNA-protein complex. I
>>> saw
>>> you posted a question titled “Atoms in the .top are not numbered
>>> consecutively from 1” on gromacs forum. I know it has been 3 years since
>>> you asked the question. I would like to know if you have solved the
>>> problem
>>> and how to fix this error?
>>>
 Hope to hear from you soon,
 Thanks,
 Thanh Le

>>>
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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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-- 
Billy Noonan*|*PhD Student*|*Bsci ( *Adv* ), IA Hon

*LinkedIn Profile

**|*   +61420 382 557

Monash Institute for Pharmaceutical Sciences ( *MIPS* )
Royal Parade, Parkville, 3052
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Re: [gmx-users] how to distance between COM of two groups of atoms?

[Justin Lemkul]

On 7/1/16 8:56 PM, Ming Tang wrote:

Thank you Justin,

I set 2 groups (start and end )in index.ndx file. each group has 3 alpha carbon 
atoms. I used the following command to calculate the distance between COM of 
those 2 groups

gmx distance -n index.ndx -select 'com of group "start" plus com of group 
"end"' -f test.pdb -s topol.tpr -oxyz dist.xvg

and got average distance:4.385, which is not correct as my protein is around 
30-nm-long.

is the command I used correct?



The value returned is the shortest periodic distance.  Use -nopbc.

-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] how to distance between COM of two groups of atoms?

[Ming Tang]

Thank you Justin,

I set 2 groups (start and end )in index.ndx file. each group has 3 alpha carbon 
atoms. I used the following command to calculate the distance between COM of 
those 2 groups

gmx distance -n index.ndx -select 'com of group "start" plus com of group 
"end"' -f test.pdb -s topol.tpr -oxyz dist.xvg

and got average distance:4.385, which is not correct as my protein is around 
30-nm-long.

is the command I used correct?
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Re: [gmx-users] how to distance between COM of two groups of atoms?

[Justin Lemkul]

On 7/1/16 7:29 PM, Ming Tang wrote:

Dear list,

I found that gmx distance can calculate distance between 2 atoms. is there a 
way to calculate distance centre of mass between 2 group of atoms?



Yes, with gmx distance.  For instance:

http://www.gromacs.org/Documentation/How-tos/Tool_Changes_for_5.0#g_dist

--
==

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] how to distance between COM of two groups of atoms?

[Ming Tang]

Dear list,

I found that gmx distance can calculate distance between 2 atoms. is there a 
way to calculate distance centre of mass between 2 group of atoms?

Thanks,
Ming
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Re: [gmx-users] Diffusion constant

[Justin Lemkul]

On 7/1/16 6:33 PM, pari lotfi wrote:

Dear all,

I saw in the different simulation that the number of restart point affect
on the D! What is the rule of restart point on the diffusion constant
calculation?
**"The diffusion constant is calculated by least squares fitting a straight
line"**

Then all the "msd" doesn't rule in fitting and D?

If yes, how do I select least squares?

**"note that t is time from the reference positions, not simulation time" **

What is reference position? Are the reference point and restart point is
the same? How can I fit on references position instead simulation time?



This is the most complete explanation of the algorithm I've seen yet:

https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2010-July/052512.html

Then read the gmx msd code and compare it to the code you wrote.

-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] Diffusion constant

[pari lotfi]

Dear all,

I saw in the different simulation that the number of restart point affect
on the D! What is the rule of restart point on the diffusion constant
calculation?

*"The diffusion constant is calculated by least squares fitting a straight
line"*

Then all the "msd" doesn't rule in fitting and D?

If yes, how do I select least squares?


*"note that t is time from the reference positions, not simulation time" *
What is reference position? Are the reference point and restart point is
the same? How can I fit on references position instead simulation time?

Thanks,
Pari
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[gmx-users] Diffusion constant

[pari lotfi]

Dear all,

I saw in the different simulation that the number of restart point affect
on the D! What is the rule of restart point on the diffusion constant
calculation?
**"The diffusion constant is calculated by least squares fitting a straight
line"**

Then all the "msd" doesn't rule in fitting and D?

If yes, how do I select least squares?

**"note that t is time from the reference positions, not simulation time" **

What is reference position? Are the reference point and restart point is
the same? How can I fit on references position instead simulation time?

Thanks in advance,
Pari
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[gmx-users] Force filed of N2 (TraPPE)

[Fei Zhang]

Hello all,

I currently ran into a problem with simulating some N2 gas between graphene
sheets using Gromacs 4.5.7. The density of N2 looks like shown below. N2
molecules tends to go near the up graphene sheet.

[image: Inline image 1]

I used the TraPPE forcefield for N2 molecules and I used PME for
electrostatic calculation.

I think there used to be an bug with PME virial while using non-linear
virtual site, but it is fixed in Gromacs 4.5.6.

Can anyone help me with this problem?

PS: itp file of N2

[ moleculetype ]

N2G   3

[ atoms ]

; nrtype   resnr residueatomcgnr  chargemass

   1  VN   1N2G   VN   1  0.964   0

   2  NN   1N2G   NN   2  -0.482 14.00670

   3  NN   1N2G   NN   3  -0.482 14.00670

[ constraints ]

2 3 2 0.110

[ virtual_sites2 ]

1 2 3 1 0.5

Regards,

Hugh
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Re: [gmx-users] Energy between desired selected molecules

[Faezeh Pousaneh]

Thank you again :)


Best regards


On Fri, Jul 1, 2016 at 4:17 PM, Justin Lemkul  wrote:

>
>
> On 7/1/16 10:05 AM, Faezeh Pousaneh wrote:
>
>> Thank you Justin and Mark for the help. I could obtain.
>>
>> More details for someone with similar question:
>>
>> 1- First I defined the molecules (resnr 1 to 4) I wanted to look at  (from
>> existing simulation: production.tpr  6000wat.gro) :
>>
>> g_select -f 6000wat.gro -s production.tpr -on index.ndx
>>
>> resnr 1 to 4
>>
>> resnr 5 to 6000
>>
>> (all other renaming molecules also must be defined as next group,
>> resnr 5 to 6000)
>>
>> 2- Then I looked at the name of groups created in the index file and
>> changed the current .mdp file to include those groups:
>>
>>
> For the sake of correctness in the archive, don't do this:
>
> tc-grps   =  resnr_5_to_6000 resnr_1_to_4
>>
>
> For the purpose of a re-run, tc-grps being split this way has no effect.
> But one should absolutely not divide thermostatting groups in this way.
>
> I feel it is important to point out so that (1) people don't make this a
> common practice and (2) you don't start re-using .mdp files with these
> settings.
>
> This is all you need to accomplish what you want in terms of the energy:
>
> energygrps=  resnr_5_to_6000resnr_1_to_4
>>
>>
> The rest of the .mdp file should be the same as your original run.
>
> -Justin
>
>
> 3- Finally rerun
>>
>> grompp -f new.mdp -c 6000wat.gro -p topol.top -o new.tpr -n index.ndx
>> mdrun -rerun traj.xtc -s new.tpr -mn index.ndx
>>
>> 4- So, if you now run g_energy you'll find those specified groups
>> energies.
>>
>>
>>
>> Best regards
>>
>>
>> On Fri, Jul 1, 2016 at 2:38 PM, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 7/1/16 8:36 AM, Faezeh Pousaneh wrote:
>>>
>>> Thank you both, I am close to solve it. The remaining problem is when I
 mdrun -rerun, it tells the number of atoms in old trajectory is not the
 same as chosen index file.

 Number of atoms in trajectory (24000) does not match the run input file

>
> (16)


 Your .tpr file needs to contain the same system that you ran before.
>>> The
>>> only thing that changes is the energygrps setting in the .mdp file.
>>>
>>> -Justin
>>>
>>>
>>> can you help me?
>>>
 Best regards


 On Fri, Jul 1, 2016 at 2:19 PM, Mark Abraham 
 wrote:

 Hi,

>
> Yes as Justin says, a group is a few molecules that you selected :-)
>
> Mark
>
> On Fri, 1 Jul 2016 14:00 Justin Lemkul  wrote:
>
>
>
>> On 7/1/16 7:55 AM, Faezeh Pousaneh wrote:
>>
>> Thank you Mark, I see. But what is the solution then? The way you
>>>
>>> proposed
>>
>>
>>> ''You can make a new .tpr file with those
>>> energy groups and use mdrun -rerun on the old trajectory, however.''
>>>
>>>  is not my answer, since I do not want the energy for a ''group'' of
>>> molecules, rather for specified combination of few molecules I define
>>>
>>> from
>>
>> g_select.
>>>
>>>
>>> The only function available is to define energygrps in the .mdp file,
>> supply an
>> index file with those groups (e.g. from g_select) and do as Mark says
>> and
>> re-calculate those interaction energies with mdrun -rerun on the
>> existing
>> trajectory.  The short-range nonbonded interaction energies between
>> those
>> groups
>> will be written to their own terms in a new .edr file.
>>
>> -Justin
>>
>>
>> Best regards
>>>
>>>
>>> On Fri, Jul 1, 2016 at 11:20 AM, Mark Abraham <
>>>
>>> mark.j.abra...@gmail.com>
>>
>
> wrote:
>>
>>>
>>> Hi,
>>>

 The .edr file contains only what was written during the simulation,

 and
>>>
>>
> that was for any energy groups defined before that run. You're trying
>>
>>>
 to
>>>
>>
> ask it to make an arbitrary repartition, which it can't do unless it
>>
>>> recorded every component of the energy for every frame (which would

 take
>>>
>>
> forever and use lots of disk). You can make a new .tpr file with those
>>
>>> energy groups and use mdrun -rerun on the old trajectory, however.

 Mark

 On Fri, Jul 1, 2016 at 9:41 AM Faezeh Pousaneh 
 wrote:

 Hi

>
> Does someone know how to obtain energy between specific molecules
> in
>
> the

>>>
>> system?
>>>

> What I did and seems not be correct is:
> 1- I obtained the molecules I wanted to look at:
> g_select_mpi -f 600gro.gro -s production.tpr -on
>
> 2- Then I produced a .tpr file for the chosen 

Re: [gmx-users] Energy between desired selected molecules

[Faezeh Pousaneh]

Thank you Justin and Mark for the help. I could obtain.

More details for someone with similar question:

1- First I defined the molecules (resnr 1 to 4) I wanted to look at  (from
existing simulation: production.tpr  6000wat.gro) :

g_select -f 6000wat.gro -s production.tpr -on index.ndx

resnr 1 to 4

resnr 5 to 6000

(all other renaming molecules also must be defined as next group,
resnr 5 to 6000)

2- Then I looked at the name of groups created in the index file and
changed the current .mdp file to include those groups:

tc-grps   =  resnr_5_to_6000 resnr_1_to_4
energygrps=  resnr_5_to_6000resnr_1_to_4

3- Finally rerun

grompp -f new.mdp -c 6000wat.gro -p topol.top -o new.tpr -n index.ndx
mdrun -rerun traj.xtc -s new.tpr -mn index.ndx

4- So, if you now run g_energy you'll find those specified groups energies.



Best regards


On Fri, Jul 1, 2016 at 2:38 PM, Justin Lemkul  wrote:

>
>
> On 7/1/16 8:36 AM, Faezeh Pousaneh wrote:
>
>> Thank you both, I am close to solve it. The remaining problem is when I
>> mdrun -rerun, it tells the number of atoms in old trajectory is not the
>> same as chosen index file.
>>
>> Number of atoms in trajectory (24000) does not match the run input file
>>>
>> (16)
>>
>>
> Your .tpr file needs to contain the same system that you ran before.  The
> only thing that changes is the energygrps setting in the .mdp file.
>
> -Justin
>
>
> can you help me?
>> Best regards
>>
>>
>> On Fri, Jul 1, 2016 at 2:19 PM, Mark Abraham 
>> wrote:
>>
>> Hi,
>>>
>>> Yes as Justin says, a group is a few molecules that you selected :-)
>>>
>>> Mark
>>>
>>> On Fri, 1 Jul 2016 14:00 Justin Lemkul  wrote:
>>>
>>>

 On 7/1/16 7:55 AM, Faezeh Pousaneh wrote:

> Thank you Mark, I see. But what is the solution then? The way you
>
 proposed

>
> ''You can make a new .tpr file with those
> energy groups and use mdrun -rerun on the old trajectory, however.''
>
>  is not my answer, since I do not want the energy for a ''group'' of
> molecules, rather for specified combination of few molecules I define
>
 from

> g_select.
>
>
 The only function available is to define energygrps in the .mdp file,
 supply an
 index file with those groups (e.g. from g_select) and do as Mark says
 and
 re-calculate those interaction energies with mdrun -rerun on the
 existing
 trajectory.  The short-range nonbonded interaction energies between
 those
 groups
 will be written to their own terms in a new .edr file.

 -Justin


> Best regards
>
>
> On Fri, Jul 1, 2016 at 11:20 AM, Mark Abraham <
>
 mark.j.abra...@gmail.com>
>>>
 wrote:
>
> Hi,
>>
>> The .edr file contains only what was written during the simulation,
>>
> and
>>>
 that was for any energy groups defined before that run. You're trying
>>
> to
>>>
 ask it to make an arbitrary repartition, which it can't do unless it
>> recorded every component of the energy for every frame (which would
>>
> take
>>>
 forever and use lots of disk). You can make a new .tpr file with those
>> energy groups and use mdrun -rerun on the old trajectory, however.
>>
>> Mark
>>
>> On Fri, Jul 1, 2016 at 9:41 AM Faezeh Pousaneh 
>> wrote:
>>
>> Hi
>>>
>>> Does someone know how to obtain energy between specific molecules in
>>>
>> the

> system?
>>>
>>> What I did and seems not be correct is:
>>> 1- I obtained the molecules I wanted to look at:
>>> g_select_mpi -f 600gro.gro -s production.tpr -on
>>>
>>> 2- Then I produced a .tpr file for the chosen selection,index.ndx,
>>> tpbconv -s production.tpr -n index.ndx -o tpxout.tpr
>>>
>>> 3- Finally put the created .tpr file as an input for g_energy
>>> g_energy -f ener.edr -s tpxout.tpr  (either, g_energy -s tpxout.tpr)
>>>
>>> But that is not the solution, since it gives energy for whole system.
>>> Best regards
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>> posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
>>>
>> or
>>>
 send a mail to gmx-users-requ...@gromacs.org.
>>>
>>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
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>>
>> * For (un)subscribe requests visit
>> 

Re: [gmx-users] Contradiction beetwen Domain Decomposition in PME and the use of SPECBOND

[Justin Lemkul]

On 7/1/16 8:50 AM, Олег Шавыкин wrote:

 Dear All,

We tried to make simulation of lysine dendrimer (with repeat unit consisting of 
one branched lysine (LYH) and two linear lysine (CLYO and LYS) in each 
generation) using SPECBOND command to create branched structure.
We use next specbond.dat file:

1
CLYOC   1   LYH NZ  1   0.151   CLYOLYH

We use PME for calculation of electrostatics interactions which use Domain 
Decomposition program.
Simulation is running well on single processor on PC using command:

mdrun -s trp_md.tpr -o trp_md.trr -c trp_pmd.gro -g md.log -e md.edr

or on 4 processors on PC using command:

mpirun -n 4 mdrun -dlb no -s trp_md.tpr -o trp_md.trr -c trp_pmd.gro -g md.log 
-e md.edr

We use here option "-dlb no", because mpirun for our task doesn't work on PC 
without it and give error message similar to that
on big computer (see below).

However, it doesn't work on supercomputer using command:

sbatch -n 64 -J task -t 5 -p test ompi 
/home/users/user1/_scratch/gromacs/bin/mdrun -dlb no -s trp_md.tpr -o traj.xtc 
-c trp_end.gro -npme 32 -v

We use same approach and the same command on supercomputer for similar molucule 
before (without SPECBOND) and it works O'K.

In the case of SPECBOND we have got next error message:

Initializing Domain Decomposition on 64 nodes
Dynamic load balancing: no
Will sort the charge groups at every domain (re)decomposition
Initial maximum inter charge-group distances:
two-body bonded interactions: 0.410 nm, LJ-14, atoms 830 838
  multi-body bonded interactions: 4.442 nm, Improper Dih., atoms 496 495


Bonded interactions should not occur over such distances; inspect the topology 
to make sure it is actually sound.  These atoms will tell you what's going on.


-Justin


Minimum cell size due to bonded interactions: 4.886 nm
Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.763 nm
Estimated maximum distance required for P-LINCS: 0.763 nm
Using 32 separate PME nodes, per user request
Optimizing the DD grid for 32 cells with a minimum initial size of 4.886 nm
The maximum allowed number of cells is: X 2 Y 2 Z 2

---
Program mdrun, VERSION 4.5.6
Source code file: domdec.c, line: 6436

Fatal error:
There is no domain decomposition for 32 nodes that is compatible with the given 
box and a minimum cell size of 4.88592 nm
Change the number of nodes or mdrun option -rdd
Look in the log file for details on the domain decomposition
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

We tried change number of nodes and used mdrun option -rdd, but without success.

We use next md.mdp:

title   =  Yo
cpp =  /usr/bin/cpp
constraints =  all-bonds
integrator  =  md
dt  =  0.002; ps !
nsteps  =  5000 ; total 100 ns.
nstcomm =  1
nstxtcout   =  1000
nstxout =  0
nstvout =  0
nstfout =  0
nstlog  =  5
nstenergy   =  5000
nstlist =  10
ns_type =  grid
coulombtype = PME
rvdw = 0.9
rlist = 0.9
rcoulomb = 0.9
fourierspacing = 0.12
pme_order = 4
ewald_rtol = 1e-5
; Berendsen temperature coupling is on in two groups
Tcoupl  =  v-rescale
tc-grps =  Protein SOL   CL
tau_t   =  0.1 0.1   0.0
ref_t   =  300 300   300
; Energy monitoring
energygrps  =  Protein SOLCL
; Isotropic pressure coupling is now on
Pcoupl  =  Parrinello-Rahman
Pcoupltype  = isotropic
tau_p   =  0.5
compressibility =  4.5e-5
ref_p   =  1.0
; Generate velocites is off at 300 K.
gen_vel =  no
gen_temp=  300.0
gen_seed=  371925

please, help us



--
==

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] fatal error in grompp

[Justin Lemkul]

On 7/1/16 9:14 AM, roshanak starlight wrote:

Hello
I'm trying to simulate the kalp-15 in dppc from gromacs Tutorial by gromacs-
4.5.5. When I run grompp  with this command : grompp -f minim.mdp -c
dppc128.gro -p topol_dppc.top -o em.tpr
I face whith this error:

Fatal error:
Syntax error - File ffnonbonded.itp, line 1
Last line read:
'[ atomtypes ]'
Invalid order for directive atomtypes

what is the reason ?



You've either constructed the topology incorrectly or assembled the force field 
incorrectly.  Follow the tutorial exactly; don't skip steps or change anything 
about it.



And an else question :is it necessary that i chang oplsaa force fileld and
chang in lipid.itp  ?
whit these descriptions:

http://lists.gromacs.org/pipermail/gromacs.org_gmx-users/2006-May/021416.html
http://lists.gromacs.org/pipermail/gromacs.org_gmx-users/2006-August/023587.html
http://lists.gromacs.org/pipermail/gromacs.org_gmx-users/2006-September/023761.html

I dont do it .could that fatal error is this?


That has nothing to do with your fatal error.  If you're trying to hack force 
fields, then you're not actually doing the tutorial and therefore whatever 
you're trying to do is incorrect, but you haven't really explained what you're 
doing.  Combining Berger lipid parameters with OPLS-AA does require the 
modifications that Chris describes in order to get an internally consistent 
force field description.


There are better (already consistent) force fields available, though.

-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] fatal error in grompp

[roshanak starlight]

Hello
I'm trying to simulate the kalp-15 in dppc from gromacs Tutorial by gromacs-
4.5.5. When I run grompp  with this command : grompp -f minim.mdp -c
dppc128.gro -p topol_dppc.top -o em.tpr
I face whith this error:

Fatal error:
Syntax error - File ffnonbonded.itp, line 1
Last line read:
'[ atomtypes ]'
Invalid order for directive atomtypes

what is the reason ?

And an else question :is it necessary that i chang oplsaa force fileld and
chang in lipid.itp  ?
whit these descriptions:

http://lists.gromacs.org/pipermail/gromacs.org_gmx-users/2006-May/021416.html
http://lists.gromacs.org/pipermail/gromacs.org_gmx-users/2006-August/023587.html
http://lists.gromacs.org/pipermail/gromacs.org_gmx-users/2006-September/023761.html

I dont do it .could that fatal error is this?
pleas guide me .thank you
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Re: [gmx-users] Energy between desired selected molecules

[Justin Lemkul]

On 7/1/16 8:36 AM, Faezeh Pousaneh wrote:

Thank you both, I am close to solve it. The remaining problem is when I
mdrun -rerun, it tells the number of atoms in old trajectory is not the
same as chosen index file.


Number of atoms in trajectory (24000) does not match the run input file

(16)



Your .tpr file needs to contain the same system that you ran before.  The only 
thing that changes is the energygrps setting in the .mdp file.


-Justin


can you help me?
Best regards


On Fri, Jul 1, 2016 at 2:19 PM, Mark Abraham 
wrote:


Hi,

Yes as Justin says, a group is a few molecules that you selected :-)

Mark

On Fri, 1 Jul 2016 14:00 Justin Lemkul  wrote:




On 7/1/16 7:55 AM, Faezeh Pousaneh wrote:

Thank you Mark, I see. But what is the solution then? The way you

proposed


''You can make a new .tpr file with those
energy groups and use mdrun -rerun on the old trajectory, however.''

 is not my answer, since I do not want the energy for a ''group'' of
molecules, rather for specified combination of few molecules I define

from

g_select.



The only function available is to define energygrps in the .mdp file,
supply an
index file with those groups (e.g. from g_select) and do as Mark says and
re-calculate those interaction energies with mdrun -rerun on the existing
trajectory.  The short-range nonbonded interaction energies between those
groups
will be written to their own terms in a new .edr file.

-Justin



Best regards


On Fri, Jul 1, 2016 at 11:20 AM, Mark Abraham <

mark.j.abra...@gmail.com>

wrote:


Hi,

The .edr file contains only what was written during the simulation,

and

that was for any energy groups defined before that run. You're trying

to

ask it to make an arbitrary repartition, which it can't do unless it
recorded every component of the energy for every frame (which would

take

forever and use lots of disk). You can make a new .tpr file with those
energy groups and use mdrun -rerun on the old trajectory, however.

Mark

On Fri, Jul 1, 2016 at 9:41 AM Faezeh Pousaneh 
wrote:


Hi

Does someone know how to obtain energy between specific molecules in

the

system?

What I did and seems not be correct is:
1- I obtained the molecules I wanted to look at:
g_select_mpi -f 600gro.gro -s production.tpr -on

2- Then I produced a .tpr file for the chosen selection,index.ndx,
tpbconv -s production.tpr -n index.ndx -o tpxout.tpr

3- Finally put the created .tpr file as an input for g_energy
g_energy -f ener.edr -s tpxout.tpr  (either, g_energy -s tpxout.tpr)

But that is not the solution, since it gives energy for whole system.
Best regards
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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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--
==

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

==
--
Gromacs Users mailing list

* 

Re: [gmx-users] Energy between desired selected molecules

[Faezeh Pousaneh]

Thank you both, I am close to solve it. The remaining problem is when I
mdrun -rerun, it tells the number of atoms in old trajectory is not the
same as chosen index file.

>Number of atoms in trajectory (24000) does not match the run input file
(16)

can you help me?
Best regards


On Fri, Jul 1, 2016 at 2:19 PM, Mark Abraham 
wrote:

> Hi,
>
> Yes as Justin says, a group is a few molecules that you selected :-)
>
> Mark
>
> On Fri, 1 Jul 2016 14:00 Justin Lemkul  wrote:
>
> >
> >
> > On 7/1/16 7:55 AM, Faezeh Pousaneh wrote:
> > > Thank you Mark, I see. But what is the solution then? The way you
> > proposed
> > >
> > > ''You can make a new .tpr file with those
> > > energy groups and use mdrun -rerun on the old trajectory, however.''
> > >
> > >  is not my answer, since I do not want the energy for a ''group'' of
> > > molecules, rather for specified combination of few molecules I define
> > from
> > > g_select.
> > >
> >
> > The only function available is to define energygrps in the .mdp file,
> > supply an
> > index file with those groups (e.g. from g_select) and do as Mark says and
> > re-calculate those interaction energies with mdrun -rerun on the existing
> > trajectory.  The short-range nonbonded interaction energies between those
> > groups
> > will be written to their own terms in a new .edr file.
> >
> > -Justin
> >
> > >
> > > Best regards
> > >
> > >
> > > On Fri, Jul 1, 2016 at 11:20 AM, Mark Abraham <
> mark.j.abra...@gmail.com>
> > > wrote:
> > >
> > >> Hi,
> > >>
> > >> The .edr file contains only what was written during the simulation,
> and
> > >> that was for any energy groups defined before that run. You're trying
> to
> > >> ask it to make an arbitrary repartition, which it can't do unless it
> > >> recorded every component of the energy for every frame (which would
> take
> > >> forever and use lots of disk). You can make a new .tpr file with those
> > >> energy groups and use mdrun -rerun on the old trajectory, however.
> > >>
> > >> Mark
> > >>
> > >> On Fri, Jul 1, 2016 at 9:41 AM Faezeh Pousaneh 
> > >> wrote:
> > >>
> > >>> Hi
> > >>>
> > >>> Does someone know how to obtain energy between specific molecules in
> > the
> > >>> system?
> > >>>
> > >>> What I did and seems not be correct is:
> > >>> 1- I obtained the molecules I wanted to look at:
> > >>> g_select_mpi -f 600gro.gro -s production.tpr -on
> > >>>
> > >>> 2- Then I produced a .tpr file for the chosen selection,index.ndx,
> > >>> tpbconv -s production.tpr -n index.ndx -o tpxout.tpr
> > >>>
> > >>> 3- Finally put the created .tpr file as an input for g_energy
> > >>> g_energy -f ener.edr -s tpxout.tpr  (either, g_energy -s tpxout.tpr)
> > >>>
> > >>> But that is not the solution, since it gives energy for whole system.
> > >>> Best regards
> > >>> --
> > >>> Gromacs Users mailing list
> > >>>
> > >>> * Please search the archive at
> > >>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > >>> posting!
> > >>>
> > >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >>>
> > >>> * For (un)subscribe requests visit
> > >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> > >>> send a mail to gmx-users-requ...@gromacs.org.
> > >>>
> > >> --
> > >> Gromacs Users mailing list
> > >>
> > >> * Please search the archive at
> > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > >> posting!
> > >>
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> > >>
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> > >> send a mail to gmx-users-requ...@gromacs.org.
> > >>
> >
> > --
> > ==
> >
> > 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
> >
> > ==
> > --
> > 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.
> >
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Re: [gmx-users] Autocorrelation function

[sun]

Allright. Thank you. 

Sent from my iPhone

> On 01-Jul-2016, at 3:37 pm, Mark Abraham  wrote:
> 
> Hi,
> 
> If an autocorrelation time is 7ps and you collect data every 20ps, can you
> observe the former correctly?
> 
> Mark
> 
>> On Fri, 1 Jul 2016 12:04 sun  wrote:
>> 
>> Hello
>> I have completed a protein ligand MD using Gromos43a1 and Gromacs v 5.0. I
>> want to know while using gmx analyze, autocorrelation graph between
>> eigenvectors is generated. However, the value is going sharply down to 0
>> and then to negative values. This probably means that something is wrong
>> with the simulation. I want to assess the stability of helical conformation
>> in the presence of ligand.
>> Secondly, I want to know what is exactly the meaning of following line:
>> Option -ac produces the autocorrelation function(s). Be sure that the time
>> interval between data points is much shorter than the time scale of the
>> autocorrelation.
>> 
>> Please someone elaborate.
>> With Regards
>> Suniba
>> 
>> Sent from my iPhone
>> --
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Re: [gmx-users] Energy between desired selected molecules

[Mark Abraham]

Hi,

Yes as Justin says, a group is a few molecules that you selected :-)

Mark

On Fri, 1 Jul 2016 14:00 Justin Lemkul  wrote:

>
>
> On 7/1/16 7:55 AM, Faezeh Pousaneh wrote:
> > Thank you Mark, I see. But what is the solution then? The way you
> proposed
> >
> > ''You can make a new .tpr file with those
> > energy groups and use mdrun -rerun on the old trajectory, however.''
> >
> >  is not my answer, since I do not want the energy for a ''group'' of
> > molecules, rather for specified combination of few molecules I define
> from
> > g_select.
> >
>
> The only function available is to define energygrps in the .mdp file,
> supply an
> index file with those groups (e.g. from g_select) and do as Mark says and
> re-calculate those interaction energies with mdrun -rerun on the existing
> trajectory.  The short-range nonbonded interaction energies between those
> groups
> will be written to their own terms in a new .edr file.
>
> -Justin
>
> >
> > Best regards
> >
> >
> > On Fri, Jul 1, 2016 at 11:20 AM, Mark Abraham 
> > wrote:
> >
> >> Hi,
> >>
> >> The .edr file contains only what was written during the simulation, and
> >> that was for any energy groups defined before that run. You're trying to
> >> ask it to make an arbitrary repartition, which it can't do unless it
> >> recorded every component of the energy for every frame (which would take
> >> forever and use lots of disk). You can make a new .tpr file with those
> >> energy groups and use mdrun -rerun on the old trajectory, however.
> >>
> >> Mark
> >>
> >> On Fri, Jul 1, 2016 at 9:41 AM Faezeh Pousaneh 
> >> wrote:
> >>
> >>> Hi
> >>>
> >>> Does someone know how to obtain energy between specific molecules in
> the
> >>> system?
> >>>
> >>> What I did and seems not be correct is:
> >>> 1- I obtained the molecules I wanted to look at:
> >>> g_select_mpi -f 600gro.gro -s production.tpr -on
> >>>
> >>> 2- Then I produced a .tpr file for the chosen selection,index.ndx,
> >>> tpbconv -s production.tpr -n index.ndx -o tpxout.tpr
> >>>
> >>> 3- Finally put the created .tpr file as an input for g_energy
> >>> g_energy -f ener.edr -s tpxout.tpr  (either, g_energy -s tpxout.tpr)
> >>>
> >>> But that is not the solution, since it gives energy for whole system.
> >>> Best regards
> >>> --
> >>> Gromacs Users mailing list
> >>>
> >>> * Please search the archive at
> >>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >>> posting!
> >>>
> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>>
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> >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >>> send a mail to gmx-users-requ...@gromacs.org.
> >>>
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> >> Gromacs Users mailing list
> >>
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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] time in restarting job

[Justin Lemkul]

On 7/1/16 8:12 AM, Marta Wisniewska wrote:

Dear Users,

I am a bit confused. I'd like extend my simulation. For it I used command:
grompp -f prod.mdp -c prod.tpr -o prod_ext.tpr -t prod.cpt
mdrun -s prod_ext.tpr

But now I have 2 simulation (first md) 0-100ns and extended 0-50ns. How to
extend time? Because after trjcat .trr files I'd like to have 150ns
simulations, not 100ns and 50ns, what I have now.



If you use grompp to extend runs, you need to change tinit and init_step, 
otherwise the run starts from t=0.  This can be corrected with trjcat -settime 
when concatenating, otherwise use the simpler approach without grompp:


http://www.gromacs.org/Documentation/How-tos/Extending_Simulations#Version_4_and_Newer

-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

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Re: [gmx-users] Energy between desired selected molecules

[Justin Lemkul]

On 7/1/16 7:55 AM, Faezeh Pousaneh wrote:

Thank you Mark, I see. But what is the solution then? The way you proposed

''You can make a new .tpr file with those
energy groups and use mdrun -rerun on the old trajectory, however.''

 is not my answer, since I do not want the energy for a ''group'' of
molecules, rather for specified combination of few molecules I define from
g_select.



The only function available is to define energygrps in the .mdp file, supply an 
index file with those groups (e.g. from g_select) and do as Mark says and 
re-calculate those interaction energies with mdrun -rerun on the existing 
trajectory.  The short-range nonbonded interaction energies between those groups 
will be written to their own terms in a new .edr file.


-Justin



Best regards


On Fri, Jul 1, 2016 at 11:20 AM, Mark Abraham 
wrote:


Hi,

The .edr file contains only what was written during the simulation, and
that was for any energy groups defined before that run. You're trying to
ask it to make an arbitrary repartition, which it can't do unless it
recorded every component of the energy for every frame (which would take
forever and use lots of disk). You can make a new .tpr file with those
energy groups and use mdrun -rerun on the old trajectory, however.

Mark

On Fri, Jul 1, 2016 at 9:41 AM Faezeh Pousaneh 
wrote:


Hi

Does someone know how to obtain energy between specific molecules in the
system?

What I did and seems not be correct is:
1- I obtained the molecules I wanted to look at:
g_select_mpi -f 600gro.gro -s production.tpr -on

2- Then I produced a .tpr file for the chosen selection,index.ndx,
tpbconv -s production.tpr -n index.ndx -o tpxout.tpr

3- Finally put the created .tpr file as an input for g_energy
g_energy -f ener.edr -s tpxout.tpr  (either, g_energy -s tpxout.tpr)

But that is not the solution, since it gives energy for whole system.
Best regards
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--
==

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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] Energy between desired selected molecules

[Faezeh Pousaneh]

Thank you Mark, I see. But what is the solution then? The way you proposed

''You can make a new .tpr file with those
energy groups and use mdrun -rerun on the old trajectory, however.''

 is not my answer, since I do not want the energy for a ''group'' of
molecules, rather for specified combination of few molecules I define from
g_select.


Best regards


On Fri, Jul 1, 2016 at 11:20 AM, Mark Abraham 
wrote:

> Hi,
>
> The .edr file contains only what was written during the simulation, and
> that was for any energy groups defined before that run. You're trying to
> ask it to make an arbitrary repartition, which it can't do unless it
> recorded every component of the energy for every frame (which would take
> forever and use lots of disk). You can make a new .tpr file with those
> energy groups and use mdrun -rerun on the old trajectory, however.
>
> Mark
>
> On Fri, Jul 1, 2016 at 9:41 AM Faezeh Pousaneh 
> wrote:
>
> > Hi
> >
> > Does someone know how to obtain energy between specific molecules in the
> > system?
> >
> > What I did and seems not be correct is:
> > 1- I obtained the molecules I wanted to look at:
> > g_select_mpi -f 600gro.gro -s production.tpr -on
> >
> > 2- Then I produced a .tpr file for the chosen selection,index.ndx,
> > tpbconv -s production.tpr -n index.ndx -o tpxout.tpr
> >
> > 3- Finally put the created .tpr file as an input for g_energy
> > g_energy -f ener.edr -s tpxout.tpr  (either, g_energy -s tpxout.tpr)
> >
> > But that is not the solution, since it gives energy for whole system.
> > Best regards
> > --
> > 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.
> >
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Re: [gmx-users] Water molecule can not be settled‏

[Mark Abraham]

Hi,

Thus your topology has a problem, e.g. wrong bond lengths or inappropriate
restraints.

Mark

On Fri, 1 Jul 2016 12:42 zeineb SI CHAIB  wrote:

> Hi Mark,
>
>
>
>
> I verified the names in the .gro files: all the names are OK!
> I also verified a C=C bond distance (within an aromatic cycle) and it is =
> 3.67 (I took a PDB file used to generate this model  and which contain the
> THF, the distance between the same atoms were 1,43!!)
>
> Zeineb
>
>
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Re: [gmx-users] Water molecule can not be settled‏

[zeineb SI CHAIB]

These VMD warnings are normal I guess, I had them when I opened another PDB 
file (that contain the THF  and it was correctly displayed!).

Zeineb



  
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Re: [gmx-users] Water molecule can not be settled‏

[zeineb SI CHAIB]

When I verified the output of VMD after opening the file I had these warnings: 

Warning) Detected a mismatch between CUDA runtime and GPU driver
Warning) Check to make sure that GPU drivers are up to date.
Info) No CUDA accelerator devices available.
Warning) Detected X11 'Composite' extension: if incorrect display occurs
Warning) try disabling this X server option.  Most OpenGL drivers
Warning) disable stereoscopic display when 'Composite' is enabled.

Regards

Zeineb


  
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Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 147, Issue 3

[zeineb SI CHAIB]

I verified the names in the .gro files: all the names are OK!
I also verified a C=C bond distance (within an aromatic cycle) and it is = 3.67 
(I took a PDB file used to generate this model  and which contain the THF, the 
distance between the same atoms were 1,43!!)

Zeineb

  
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Re: [gmx-users] md with multiple ligands

[Justin Lemkul]

On 6/30/16 11:22 PM, Billy Williams-Noonan wrote:

Hi Thanh,

Maybe try to check if the numbering of your atoms in the topology files is
consistent with the .pdb or .gro files they describe.



Coordinate file and topology file numbering are different and use different 
conventions.  In fact, if one numbers a topology using global atom numbers from 
a coordinate file, it is what causes the error the OP reports.  Each 
[moleculetype] directive must be numbered consecutively from 1; after that, the 
only match with the coordinate file is based on the correct appearance of atom 
names (thus a link between [molecules] in the .top and the coordinates themselves).


-Justin


Billy

On 1 July 2016 at 09:20, Thanh Le  wrote:




On Jun 30, 2016, at 3:48 PM, Thanh Le  wrote:

My name is Thanh Le, a graduate student in chemistry. Currently, I am

using gromacs to do a dynamics simulation for my RNA-protein complex. I saw
you posted a question titled “Atoms in the .top are not numbered
consecutively from 1” on gromacs forum. I know it has been 3 years since
you asked the question. I would like to know if you have solved the problem
and how to fix this error?

Hope to hear from you soon,
Thanks,
Thanh Le


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==

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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

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Re: [gmx-users] Autocorrelation function

[Mark Abraham]

Hi,

If an autocorrelation time is 7ps and you collect data every 20ps, can you
observe the former correctly?

Mark

On Fri, 1 Jul 2016 12:04 sun  wrote:

> Hello
> I have completed a protein ligand MD using Gromos43a1 and Gromacs v 5.0. I
> want to know while using gmx analyze, autocorrelation graph between
> eigenvectors is generated. However, the value is going sharply down to 0
> and then to negative values. This probably means that something is wrong
> with the simulation. I want to assess the stability of helical conformation
> in the presence of ligand.
> Secondly, I want to know what is exactly the meaning of following line:
> Option -ac produces the autocorrelation function(s). Be sure that the time
> interval between data points is much shorter than the time scale of the
> autocorrelation.
>
> Please someone elaborate.
> With Regards
> Suniba
>
> Sent from my iPhone
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[gmx-users] Autocorrelation function

[sun]

Hello
I have completed a protein ligand MD using Gromos43a1 and Gromacs v 5.0. I want 
to know while using gmx analyze, autocorrelation graph between eigenvectors is 
generated. However, the value is going sharply down to 0 and then to negative 
values. This probably means that something is wrong with the simulation. I want 
to assess the stability of helical conformation in the presence of ligand. 
Secondly, I want to know what is exactly the meaning of following line:
Option -ac produces the autocorrelation function(s). Be sure that the time 
interval between data points is much shorter than the time scale of the 
autocorrelation.

Please someone elaborate.
With Regards
Suniba

Sent from my iPhone
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Re: [gmx-users] Water molecule can not be settled

[Mark Abraham]

Hi,

That looks strange, but VMD chooses its representations based on guesses
about atom names and distances, so it's quite possible to confuse it. I'd
look at VMD's console log to see whether it's complaining about anything.

Alternatively, the names and types are real and they're really that far
apart because that's what your model physics said. Find a single C-C bond
and measure its distance.

Mark

On Fri, Jul 1, 2016 at 11:25 AM zeineb SI CHAIB 
wrote:

> Dear Mark,
>
> Again, thank you very much for your orientation.
>
> I suceeded in running a minimisation in vaccuo (just after pdb2gmx) with
> the following command line:
>
> gmx mdrun -ntmpi 1 -v -deffnm protein_invacuo -s protein_invacuo.tpr
>
> The mdp parameters were:
>
> integrator = steep
> nsteps = 1500
> emtol = 1000.0
> emstep = 0.01
> energygrps= system
>
> pbc = no
> nstlist = 0
> ns-type = simple
> rlist   = 0
>
> cutoff-scheme = group
> coulombtype  = cut-off
> rcoulomb = 0
> vdw-type = Cut-off
> rvdw = 0
>
> During minimisation, I had no error and Steepest Descents converged to
> Fmax < 1000 in 389 steps
> Potential Energy  = -8.8386008e+04
> Maximum force =  9.7354883e+02 on atom 3974
> Norm of force =  4.0786911e+01
>
> However,
>  when I visualised the .gro file generated after minimisation, in VMD,
> It can't correctly display the parametrized molecule (THF). For example,
>  for a representation in licorice, I had this (right and left are HEM
> and in the center is my THF!!):
>
> https://www.dropbox.com/s/xrxw473pywbiz1s/THG_problem.png?dl=0
>
> NB: my input structure has been obtained by homology modelling using
> MODELLER but I don't think that the problem is here because I already run
> an MD of 5ns with this structure but I added the topology of THF manually
> (like in bevanlab tutorial)!?
>
> What do you think happened?
>
> Regards.
>
> Zeineb
>
>
>
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Re: [gmx-users] Energy between desired selected molecules

[Mark Abraham]

Hi,

The .edr file contains only what was written during the simulation, and
that was for any energy groups defined before that run. You're trying to
ask it to make an arbitrary repartition, which it can't do unless it
recorded every component of the energy for every frame (which would take
forever and use lots of disk). You can make a new .tpr file with those
energy groups and use mdrun -rerun on the old trajectory, however.

Mark

On Fri, Jul 1, 2016 at 9:41 AM Faezeh Pousaneh  wrote:

> Hi
>
> Does someone know how to obtain energy between specific molecules in the
> system?
>
> What I did and seems not be correct is:
> 1- I obtained the molecules I wanted to look at:
> g_select_mpi -f 600gro.gro -s production.tpr -on
>
> 2- Then I produced a .tpr file for the chosen selection,index.ndx,
> tpbconv -s production.tpr -n index.ndx -o tpxout.tpr
>
> 3- Finally put the created .tpr file as an input for g_energy
> g_energy -f ener.edr -s tpxout.tpr  (either, g_energy -s tpxout.tpr)
>
> But that is not the solution, since it gives energy for whole system.
> Best regards
> --
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Re: [gmx-users] Query regarding all-atom simulations on 980 Ti GPUs

[Mark Abraham]

On Fri, Jul 1, 2016 at 5:44 AM Suhani Nagpal 
wrote:

> Greetings
>
> I have just recently started to work on this workstation (details as shown
> below) and have employed all-atom simulation of 30,000 atoms with this
> command (just for 1 micro-sec),
>
> gmx mdrun -deffnm md -v -ntmpi 2 -ntomp 6 -gpu_id 01 -pin on
>
>
> Running on 1 node with total 8 cores, 16 logical cores, 2 compatible GPUs
> Hardware detected:
>   CPU info:
> Vendor: GenuineIntel
> Brand:  Intel(R) Core(TM) i7-5960X CPU @ 3.00GHz
> SIMD instructions most likely to fit this hardware: AVX2_256
> SIMD instructions selected at GROMACS compile time: AVX2_256
>   GPU info:
> Number of GPUs detected: 2
> #0: NVIDIA GeForce GTX 980 Ti, compute cap.: 5.2, ECC:  no, stat:
> compatible
> #1: NVIDIA GeForce GTX 980 Ti, compute cap.: 5.2, ECC:  no, stat:
> compatible
>
> Reading file md.tpr, VERSION 5.1.2 (single precision)
> Using 2 MPI threads
> Using 6 OpenMP threads per tMPI thread
>
> 2 GPUs user-selected for this run.
> Mapping of GPU IDs to the 2 PP ranks in this node: 0,1
>
>
>
> I have just given the command,
>
> and it shows:
>
> step 126800, will finish Tue Jul 12 16:11:59 2016imb F  3%
>
>
> and the imb F increases till 25-28%.
>
> According to the time, this gives a performance of less 100 ns per day.
> Because I have read other benchmarking studies, it should give above 200 ns
> at least.
>

OK, but there's nothing to go upon here. Your simulation should be running
well, but you need to start by inspecting the tail of the log file to see
what mdrun thought might be improved.


> On another note (very strange),
>
> when I subject more than 1 simulation (around 30,000 atoms) on this system,
> the performance reduces a lot (~ 50 ns per day for the second trajectory).
> and
> pin off when running more than one simulation.
>
> What am I doing wrong? I have not worked on GPUs before.
>

That's not unique to GPUs, you'll see the same kind of behaviour if you run
a CPU job (e.g. the same job with mdrun -nb cpu). mdrun performance on a
single node is "compute bound," and cannot share compute resources with
anything else and maintain performance - particularly not another mdrun.
Background information and examples for node sharing can be found at
http://manual.gromacs.org/documentation/5.1.2/user-guide/mdrun-performance.html#running-mdrun-within-a-single-node

Mark


> Kindly help
>
> Thanks a lot
>
> Suhani
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[gmx-users] Energy between desired selected molecules

[Faezeh Pousaneh]

Hi

Does someone know how to obtain energy between specific molecules in the
system?

What I did and seems not be correct is:
1- I obtained the molecules I wanted to look at:
g_select_mpi -f 600gro.gro -s production.tpr -on

2- Then I produced a .tpr file for the chosen selection,index.ndx,
tpbconv -s production.tpr -n index.ndx -o tpxout.tpr

3- Finally put the created .tpr file as an input for g_energy
g_energy -f ener.edr -s tpxout.tpr  (either, g_energy -s tpxout.tpr)

But that is not the solution, since it gives energy for whole system.
Best regards
-- 
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