date:20171206

[gmx-users] output - em.gro looks very strange

2017-12-06 Thread MD

Hi Gromacs folks,

After fixing the non-even charge issues I met new problems when running
em.mdp.
The grompp worked and mdrun em worked as well with warning, but I found the
output em.gro looks very strange with several amino acids stretched to the
other side of the box. I had the command followed with log file. Any help
would be greatly appreciated.

I looked at the distance between 4641 and 4657 in solv_ions.gro and it is
actually 11.354A. I am not quite sure about the warning message.

Thanks,

Ming




*gmx grompp -f em.mdp -c solv_ions.gro -p topol.top -o em.tpr*

GROMACS:  gmx grompp, VERSION 5.1.2
Executable:   /usr/bin/gmx
Data prefix:  /usr
Command line:
  gmx grompp -f em_real.mdp -c solv_ions.gro -p topol.top -o em.tpr

Ignoring obsolete mdp entry 'title'

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.5#

NOTE 1 [file em_real.mdp]:
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
  that with the Verlet scheme, nstlist has no effect on the accuracy of
  your simulation.

Setting the LD random seed to 2763204595 <(276)%20320-4595>
Generated 97877 of the 97903 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 64492 of the 97903 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
Excluding 3 bonded neighbours molecule type 'Ion_chain_A2'
Excluding 3 bonded neighbours molecule type 'Other_chain_B'
Excluding 3 bonded neighbours molecule type 'Protein_chain_C'
Excluding 2 bonded neighbours molecule type 'SOL'
Excluding 1 bonded neighbours molecule type 'NA'
Removing all charge groups because cutoff-scheme=Verlet
Analysing residue names:
There are:   345Protein residues
There are:11Ion residues
There are: 1  Other residues
There are: 18021  Water residues
Analysing Protein...
Analysing residues not classified as Protein/DNA/RNA/Water and splitting
into groups...
Analysing residues not classified as Protein/DNA/RNA/Water and splitting
into groups...
Number of degrees of freedom in T-Coupling group rest is 179214.00
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 80x80x80, spacing 0.119 0.119 0.119
Estimate for the relative computational load of the PME mesh part: 0.20
This run will generate roughly 5 Mb of data

There was 1 note

Back Off! I just backed up em.tpr to ./#em.tpr.3#



*gmx mdrun -v -deffnm em*

Reading file em.tpr, VERSION 5.1.2 (single precision)
Using 1 MPI thread
Using 6 OpenMP threads


Back Off! I just backed up em.trr to ./#em.trr.2#

Back Off! I just backed up em.edr to ./#em.edr.2#

Steepest Descents:
   Tolerance (Fmax)   =  1.0e+03
   Number of steps=5

WARNING: Listed nonbonded interaction between particles 4641 and 4657
at distance 2.141 which is larger than the table limit 2.000 nm.

This is likely either a 1,4 interaction, or a listed interaction inside
a 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 will
only see this message once, even if it occurs for several interactions.

IMPORTANT: This should not happen in a stable simulation, so there is
probably something wrong with your system. Only change the table-extension
distance in the mdp file if you are really sure that is the reason.


*em.mdp*

; LINES STARTING WITH ';' ARE COMMENTS
title = Minimization ; Title of run
 define=-DFLEXIBLE

; Parameters describing what to do, when to stop and what to save
integrator = steep ; Algorithm (steep = steepest descent minimization)
emtol = 1000.0   ; Stop minimization when the maximum force < 10.0 kJ/mol
emstep  = 0.01  ; Energy step size
nsteps = 5; Maximum number of (minimization) steps to perform
energygrps = Protein  ; Which energy group(s) to write to disk

; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
nstlist = 1 ; Frequency to update the neighbor list and long range
forces
cutoff-scheme   = Verlet
ns_type = grid ; Method to determine neighbor list (simple, grid)
rlist = 1.0 ; Cut-off for making neighbor list (short range forces)
coulombtype = PME ; Treatment of long range electrostatic interactions
rcoulomb = 1.0 ; long range electrostatic cut-off
rvdw = 1.0 ; long range Van der Waals cut-off
pbc = xyz  ; Periodic Boundary Conditions
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[gmx-users] non-bonded potential

2017-12-06 Thread Velia Minicozzi


Dear gromacs-users,

is there a possibility, without changing GROMACS code, to insert in GROMACS

a non-bonded potential with 6 parameters?

I have understood I can use only two parameters non-bonded potentials by 
building


tables but maybe there is a way to insert a more complicated non-bonded 
potential


with a LJ like with 4 parameters plus a Buckingham like.

Thank you,

Velia

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[gmx-users] g_sham experimental weighting with temperature

2017-12-06 Thread Yasser Bruno Ruiz Blanco

Dear,

Please could you suggest me some reference or description about the
mentioned "experimental energy and temperature weighting" of g_sham tool?

Can I safely use this energy and Temperature weighting procedure to obtain
reliable PMF plots from a T-REMD simulation?

In case of using g_sham with the weighting option, would be better to apply
the weighting using the Total energy and the Temperature of structures from
different replicas, or only the Potential energy of the structures sampled
at the temperature of interest?

Thanks in advance for your suggestions!
Y.
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[gmx-users] Using custom potential for electrostatics between protein and water

2017-12-06 Thread Aram Davtyan

Ok, so I tried the following. I have changed cutoff-scheme=verlet" to
"cutoff-scheme=group" and "rlist = 1.2" to "rlist = 1.4".

Now I get the following working when trying to generate the TPR:

WARNING 1 [file md_energygrp-table_group.mdp]:
  The sum of the two largest charge group radii (32.555389) is larger than
  rlist (1.40)

Thanks,

Aram

Hi Arm,
>
>
> As mark suggested you have to replace "cutoff-scheme=verlet" to
> "cutoff-scheme=group".
>
>
> Srinivasa
>
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Aram
> Davtyan 
> Sent: 06 December 2017 13:57:17
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: Re: [gmx-users] Using custom potential for electrostatics between
> protein and water
>
> Hi,
>
> Yeah, but first of all it doesn't give me an error and, second, how do I
> transition from verlet to group cutoff scheme in order for the custom
> tables to work?
>
> In other words, what specific changes should I make for GROMACS to use the
> modified tables, and, at the same time, when the
> `table6-12_Protein_Water.xvg` is the same as `table6-12.xvg` I get the same
> answer as before?
>
> Thanks,
>
> Aram
>
>
>
> > Hi,
> >
> > User tables for nonbonded interactions, including pme-user are only
> > supported with the group cutoff scheme, not verlet. grompp should give a
> > fatal error to tell you that, sorry.
> >
> > Mark
> >
> > On Wed, Dec 6, 2017 at 10:50 AM Aram Davtyan 
> > wrote:
> >
> > > Hello,
> > >
> > > I am trying to use a custom electrostatic potential between protein and
> > > water, with protein-protein and water-water potentials remaining the
> > same.
> > >
> > > I tried running the simulation with the following input script:
> > >
> > > define  = -DPOSRES   ; position restrain for protein
> > > integrator  = md
> > > dt  = 0.002
> > > nsteps  = 1 ; 2ns
> > > nstlog  = 1000
> > > nstxout = 5000
> > > nstvout = 5000
> > > nstfout = 5000
> > > nstcalcenergy   = 100
> > > nstenergy   = 1000
> > > ;
> > > cutoff-scheme   = Verlet
> > > nstlist = 20
> > > rlist   = 1.2
> > > coulombtype = pme-user
> > > rcoulomb= 1.2
> > > vdwtype = Cut-off
> > > vdw-modifier= Force-switch
> > > rvdw_switch = 1.0
> > > rvdw= 1.2
> > > ;
> > > energygrps  = Protein Water Ion
> > > energygrp-table = Protein Water
> > > ;
> > > tcoupl  = Nose-Hoover
> > > tc_grps = Protein Non-Protein
> > > tau_t   = 1.0 1.0
> > > ref_t   = 300.0   300.0
> > > ;
> > > pcoupl  = Parrinello-Rahman
> > > pcoupltype  = isotropic
> > > tau_p   = 5.0
> > > compressibility = 4.5e-5
> > > ref_p   = 1.0
> > > ;
> > > ld_seed = 0
> > > ;
> > > constraints = h-bonds
> > > constraint_algorithm= LINCS
> > > continuation= yes
> > > ;
> > > nstcomm = 100
> > > comm_mode   = linear
> > > comm_grps   = Protein Non-Protein
> > > ;
> > > refcoord_scaling= com
> > >
> > > I have the following tables: `table6-12.xvg` and
> > > `table6-12_Protein_Water.xvg` in the directory and run the simulation
> > with
> > > the following command lines
> > >
> > > gmx grompp -f md_energygrp-table.mdp -c npt.gro -t npt.cpt -p topol.top
> > -o
> > > md_0_5.tpr
> > > gmx mdrun -deffnm md_0_5 -reprod -table table6-12.xvg -tablep
> > table6-12.xvg
> > >
> > > To test I set the electrostatic potential (f(r) and f'(r)) to zero in
> > > `table6-12_Protein_Water.xvg` file. However, I find that the energies
> > > calculated at the first step are identical to the case when custom
> > > potentials are not used. What am I doing wrong?
> > >
> > > Thank you in advance,
> > >
> > > Aram
> > > --
> > > 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.
> > >
> >
> >
> > --
> >
> > Message: 5
> > Date: Wed, 06 Dec 2017 00:46:51 +
> > From: Mark Abraham 
> > To: gmx-us...@gromacs.org
> > Cc: gromacs.org_gmx-users@maillist.sys.kth.se
> > Subject: Re: [gmx-users] Using custom potential for electrostatics
> > between protein and water
> > Message-ID:
> >

Re: [gmx-users] Using custom potential for electrostatics between protein and water

2017-12-06 Thread Aram Davtyan

Is that really the only thing that would need to be changed to switch from
verlet to group scheme? Because to my understanding `group` works in a
different way and a buffer (skin) cutoff needs to be added. But I am not at
all sure how to do that.

Thanks,

Aram


> Hi Arm,
>
>
> As mark suggested you have to replace "cutoff-scheme=verlet" to
> "cutoff-scheme=group".
>
>
> Srinivasa
>
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Aram
> Davtyan 
> Sent: 06 December 2017 13:57:17
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: Re: [gmx-users] Using custom potential for electrostatics between
> protein and water
>
> Hi,
>
> Yeah, but first of all it doesn't give me an error and, second, how do I
> transition from verlet to group cutoff scheme in order for the custom
> tables to work?
>
> In other words, what specific changes should I make for GROMACS to use the
> modified tables, and, at the same time, when the
> `table6-12_Protein_Water.xvg` is the same as `table6-12.xvg` I get the same
> answer as before?
>
> Thanks,
>
> Aram
>
>
>
> > Hi,
> >
> > User tables for nonbonded interactions, including pme-user are only
> > supported with the group cutoff scheme, not verlet. grompp should give a
> > fatal error to tell you that, sorry.
> >
> > Mark
> >
> > On Wed, Dec 6, 2017 at 10:50 AM Aram Davtyan 
> > wrote:
> >
> > > Hello,
> > >
> > > I am trying to use a custom electrostatic potential between protein and
> > > water, with protein-protein and water-water potentials remaining the
> > same.
> > >
> > > I tried running the simulation with the following input script:
> > >
> > > define  = -DPOSRES   ; position restrain for protein
> > > integrator  = md
> > > dt  = 0.002
> > > nsteps  = 1 ; 2ns
> > > nstlog  = 1000
> > > nstxout = 5000
> > > nstvout = 5000
> > > nstfout = 5000
> > > nstcalcenergy   = 100
> > > nstenergy   = 1000
> > > ;
> > > cutoff-scheme   = Verlet
> > > nstlist = 20
> > > rlist   = 1.2
> > > coulombtype = pme-user
> > > rcoulomb= 1.2
> > > vdwtype = Cut-off
> > > vdw-modifier= Force-switch
> > > rvdw_switch = 1.0
> > > rvdw= 1.2
> > > ;
> > > energygrps  = Protein Water Ion
> > > energygrp-table = Protein Water
> > > ;
> > > tcoupl  = Nose-Hoover
> > > tc_grps = Protein Non-Protein
> > > tau_t   = 1.0 1.0
> > > ref_t   = 300.0   300.0
> > > ;
> > > pcoupl  = Parrinello-Rahman
> > > pcoupltype  = isotropic
> > > tau_p   = 5.0
> > > compressibility = 4.5e-5
> > > ref_p   = 1.0
> > > ;
> > > ld_seed = 0
> > > ;
> > > constraints = h-bonds
> > > constraint_algorithm= LINCS
> > > continuation= yes
> > > ;
> > > nstcomm = 100
> > > comm_mode   = linear
> > > comm_grps   = Protein Non-Protein
> > > ;
> > > refcoord_scaling= com
> > >
> > > I have the following tables: `table6-12.xvg` and
> > > `table6-12_Protein_Water.xvg` in the directory and run the simulation
> > with
> > > the following command lines
> > >
> > > gmx grompp -f md_energygrp-table.mdp -c npt.gro -t npt.cpt -p topol.top
> > -o
> > > md_0_5.tpr
> > > gmx mdrun -deffnm md_0_5 -reprod -table table6-12.xvg -tablep
> > table6-12.xvg
> > >
> > > To test I set the electrostatic potential (f(r) and f'(r)) to zero in
> > > `table6-12_Protein_Water.xvg` file. However, I find that the energies
> > > calculated at the first step are identical to the case when custom
> > > potentials are not used. What am I doing wrong?
> > >
> > > Thank you in advance,
> > >
> > > Aram
> > > --
> > > 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.
> > >
> >
> >
> > --
> >
> > Message: 5
> > Date: Wed, 06 Dec 2017 00:46:51 +
> > From: Mark Abraham 
> > To: gmx-us...@gromacs.org
> > Cc: gromacs.org_gmx-users@maillist.sys.kth.se
> > Subject: Re: [gmx-users] Using custom potential for electrostatics
> > between protein and water
> > Message-ID:
> >

Re: [gmx-users] Using custom potential for electrostatics between protein and water

2017-12-06 Thread Srinivasa Ramisetti

Hi Arm,


As mark suggested you have to replace "cutoff-scheme=verlet" to 
"cutoff-scheme=group".


Srinivasa


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Aram Davtyan 

Sent: 06 December 2017 13:57:17
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Re: [gmx-users] Using custom potential for electrostatics between 
protein and water

Hi,

Yeah, but first of all it doesn't give me an error and, second, how do I
transition from verlet to group cutoff scheme in order for the custom
tables to work?

In other words, what specific changes should I make for GROMACS to use the
modified tables, and, at the same time, when the
`table6-12_Protein_Water.xvg` is the same as `table6-12.xvg` I get the same
answer as before?

Thanks,

Aram



> Hi,
>
> User tables for nonbonded interactions, including pme-user are only
> supported with the group cutoff scheme, not verlet. grompp should give a
> fatal error to tell you that, sorry.
>
> Mark
>
> On Wed, Dec 6, 2017 at 10:50 AM Aram Davtyan 
> wrote:
>
> > Hello,
> >
> > I am trying to use a custom electrostatic potential between protein and
> > water, with protein-protein and water-water potentials remaining the
> same.
> >
> > I tried running the simulation with the following input script:
> >
> > define  = -DPOSRES   ; position restrain for protein
> > integrator  = md
> > dt  = 0.002
> > nsteps  = 1 ; 2ns
> > nstlog  = 1000
> > nstxout = 5000
> > nstvout = 5000
> > nstfout = 5000
> > nstcalcenergy   = 100
> > nstenergy   = 1000
> > ;
> > cutoff-scheme   = Verlet
> > nstlist = 20
> > rlist   = 1.2
> > coulombtype = pme-user
> > rcoulomb= 1.2
> > vdwtype = Cut-off
> > vdw-modifier= Force-switch
> > rvdw_switch = 1.0
> > rvdw= 1.2
> > ;
> > energygrps  = Protein Water Ion
> > energygrp-table = Protein Water
> > ;
> > tcoupl  = Nose-Hoover
> > tc_grps = Protein Non-Protein
> > tau_t   = 1.0 1.0
> > ref_t   = 300.0   300.0
> > ;
> > pcoupl  = Parrinello-Rahman
> > pcoupltype  = isotropic
> > tau_p   = 5.0
> > compressibility = 4.5e-5
> > ref_p   = 1.0
> > ;
> > ld_seed = 0
> > ;
> > constraints = h-bonds
> > constraint_algorithm= LINCS
> > continuation= yes
> > ;
> > nstcomm = 100
> > comm_mode   = linear
> > comm_grps   = Protein Non-Protein
> > ;
> > refcoord_scaling= com
> >
> > I have the following tables: `table6-12.xvg` and
> > `table6-12_Protein_Water.xvg` in the directory and run the simulation
> with
> > the following command lines
> >
> > gmx grompp -f md_energygrp-table.mdp -c npt.gro -t npt.cpt -p topol.top
> -o
> > md_0_5.tpr
> > gmx mdrun -deffnm md_0_5 -reprod -table table6-12.xvg -tablep
> table6-12.xvg
> >
> > To test I set the electrostatic potential (f(r) and f'(r)) to zero in
> > `table6-12_Protein_Water.xvg` file. However, I find that the energies
> > calculated at the first step are identical to the case when custom
> > potentials are not used. What am I doing wrong?
> >
> > Thank you in advance,
> >
> > Aram
> > --
> > 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.
> >
>
>
> --
>
> Message: 5
> Date: Wed, 06 Dec 2017 00:46:51 +
> From: Mark Abraham 
> To: gmx-us...@gromacs.org
> Cc: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: Re: [gmx-users] Using custom potential for electrostatics
> between protein and water
> Message-ID:
>

[gmx-users] different pull force constants

2017-12-06 Thread Srinivasa Ramisetti

Dear all,


I am using two different pulling constants (pull_coord1_k) to generate the 20 
configurations to extract the potential of mean force (PMF) using gmx wham. For 
instance I used pull_coord1_k =1 and 5000 for the reaction coordinates 
0.4

Re: [gmx-users] Using custom potential for electrostatics between protein and water

2017-12-06 Thread Aram Davtyan

Hi,

Yeah, but first of all it doesn't give me an error and, second, how do I
transition from verlet to group cutoff scheme in order for the custom
tables to work?

In other words, what specific changes should I make for GROMACS to use the
modified tables, and, at the same time, when the
`table6-12_Protein_Water.xvg` is the same as `table6-12.xvg` I get the same
answer as before?

Thanks,

Aram



> Hi,
>
> User tables for nonbonded interactions, including pme-user are only
> supported with the group cutoff scheme, not verlet. grompp should give a
> fatal error to tell you that, sorry.
>
> Mark
>
> On Wed, Dec 6, 2017 at 10:50 AM Aram Davtyan 
> wrote:
>
> > Hello,
> >
> > I am trying to use a custom electrostatic potential between protein and
> > water, with protein-protein and water-water potentials remaining the
> same.
> >
> > I tried running the simulation with the following input script:
> >
> > define  = -DPOSRES   ; position restrain for protein
> > integrator  = md
> > dt  = 0.002
> > nsteps  = 1 ; 2ns
> > nstlog  = 1000
> > nstxout = 5000
> > nstvout = 5000
> > nstfout = 5000
> > nstcalcenergy   = 100
> > nstenergy   = 1000
> > ;
> > cutoff-scheme   = Verlet
> > nstlist = 20
> > rlist   = 1.2
> > coulombtype = pme-user
> > rcoulomb= 1.2
> > vdwtype = Cut-off
> > vdw-modifier= Force-switch
> > rvdw_switch = 1.0
> > rvdw= 1.2
> > ;
> > energygrps  = Protein Water Ion
> > energygrp-table = Protein Water
> > ;
> > tcoupl  = Nose-Hoover
> > tc_grps = Protein Non-Protein
> > tau_t   = 1.0 1.0
> > ref_t   = 300.0   300.0
> > ;
> > pcoupl  = Parrinello-Rahman
> > pcoupltype  = isotropic
> > tau_p   = 5.0
> > compressibility = 4.5e-5
> > ref_p   = 1.0
> > ;
> > ld_seed = 0
> > ;
> > constraints = h-bonds
> > constraint_algorithm= LINCS
> > continuation= yes
> > ;
> > nstcomm = 100
> > comm_mode   = linear
> > comm_grps   = Protein Non-Protein
> > ;
> > refcoord_scaling= com
> >
> > I have the following tables: `table6-12.xvg` and
> > `table6-12_Protein_Water.xvg` in the directory and run the simulation
> with
> > the following command lines
> >
> > gmx grompp -f md_energygrp-table.mdp -c npt.gro -t npt.cpt -p topol.top
> -o
> > md_0_5.tpr
> > gmx mdrun -deffnm md_0_5 -reprod -table table6-12.xvg -tablep
> table6-12.xvg
> >
> > To test I set the electrostatic potential (f(r) and f'(r)) to zero in
> > `table6-12_Protein_Water.xvg` file. However, I find that the energies
> > calculated at the first step are identical to the case when custom
> > potentials are not used. What am I doing wrong?
> >
> > Thank you in advance,
> >
> > Aram
> > --
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>
>
> --
>
> Message: 5
> Date: Wed, 06 Dec 2017 00:46:51 +
> From: Mark Abraham 
> To: gmx-us...@gromacs.org
> Cc: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: Re: [gmx-users] Using custom potential for electrostatics
> between protein and water
> Message-ID:
>

Re: [gmx-users] How the index is recognised for values more than 99999?

2017-12-06 Thread ZHANG Cheng

Hi Mark,
I only calculate the RMSD for a particular group. So I need to use a index 
file, which explicitly indicates the atom indices within that group.


1) So if that group indices contain "1 2 3 ...", the Gromacs software will 
always assume they are 1st, 2nd, 3rd, ... atoms, instead of 11th, 12th, 
13th, ... ?


2) And if I want the RMSD for the group containing atom 11th, 12th, 
13th, ..., I need to write their indices as 11, 12, 13, ..., ?


Thank you.


Cheng




-- Original --
From:  "Mark Abraham";;
Date:  Wed, Dec 6, 2017 04:34 AM
To:  "gmx-users";
Cc:  "gromacs.org_gmx-users"; "ZHANG 
Cheng"<272699...@qq.com>; 
Subject:  Re: [gmx-users] How the index is recognised for values more than 
9?




Hi,
 
The numbering of the coordinate file is not significant for this, precisely for 
that reason.
 
Mark
 
On Wed, Dec 6, 2017, 7:20 AM ZHANG Cheng <272699...@qq.com> wrote:

Dear Gromacs,I am doing the RMSD calculation for a particular group of protein 
residues. My system also has water molecules so there are more than 9 
atoms. Thus, the 10th atom is indexed as 0, and 11th atom as 1, and so 
on.
 
 
 So if the index file for my group has an entry of 1, how can the gromacs know 
it is the 1st atom, instead of the 11th atom?
 
 
 Thank you.
 
 
 Yours sincerely
 Cheng
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[gmx-users] Unable to write whole trajectory with trjconv and error in gmx check

2017-12-06 Thread Dasgupta, R.

Dear All,

I am facing problem with GROMACS version 2016.1 and 2016.3. I gave a run of 
30ns of my protein in our local cluster that uses sbatch to queue the job. My 
input file for the sbatch is the following:


#!/bin/bash

#SBATCH -t 5-00:00:00

#SBATCH -N 4

#SBATCH --ntasks-per-node=12


export GMX_MAXBACKUP=-1 (this is required because of multiple backup files 
gromacs makes)


srun -n 4 /home/dasgupta/gromacs/bin/gmx mdrun -v -deffnm 2my9_nseed


Everything went smoothly neither the .out file did not show any error nor the 
.log file did not show any inconsistency. The problem started when I used gmx 
trjconv to extract the trajectory and make the .pdb file for visualisation. 
After just 1ns it was unable to write any other frames. So, I tried to check 
the trajectory file by the following command:


gmx check -f xxx.trr


This is the error I got:


Program: gmx check, version 2016.3

Source file: src/gromacs/fileio/trrio.cpp (line 114)


Fatal error:

Failed to find GROMACS magic number in trr frame header, so this is not a trr

file!


Before this error there was this output (just a portion of the output is shown 
here):


Timesteps at t=1159 don't match (1, 9)


Timesteps at t=1168 don't match (9, 1)


Timesteps at t=1170 don't match (1, -7)


Timesteps at t=1163 don't match (-7, 1)


Timesteps at t=1165 don't match (1, 9)


Timesteps at t=1174 don't match (9, 1)

Reading frame1200 time 1183.000

Timesteps at t=1183 don't match (1, -7)


Timesteps at t=1176 don't match (-7, 1)


Timesteps at t=1179 don't match (1, 4)


Timesteps at t=1183 don't match (4, 1)


Timesteps at t=1186 don't match (1, 3)


Timesteps at t=1189 don't match (3, 1)

Warning at frame 1211: coordinates for atom 1390 are large (7.68295e+31)

Warning at frame 1211: coordinates for atom 1391 are large (2.75578e+23)

Warning at frame 1211: there are 4 particles with all coordinates zero


I will appreciate if anyone can help me in solving this problem.


Thank you very much in advance.


Rubin Dasgupta,

Phd Student,

Leiden University,

The Netherlands.
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[gmx-users] RADIAL DISTRIBUTION FUNTION

2017-12-06 Thread Neha Gupta

Hi gromacs users,

Through my RDF graph, I want to ascertain that my molecule of interest is a
solid. How to observe that?

I get r (nm) in X-aix and g(r) in Y-axis.

But, in some graphs, I observe r/sigma along X-axis.

Which is correct?

Thanks,
Neha
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Re: [gmx-users] Insertion of Ion-channels onto the membrane using g_membed with Amber force field

2017-12-06 Thread Mark Abraham

Hi,

I'd start by considering the options at
http://manual.gromacs.org/documentation/2016.4/user-guide/mdrun-features.html#running-a-membrane-protein-embedding-simulation

Mark

On Wed, Dec 6, 2017, 6:12 PM Dhaniram Mahato  wrote:

> Thanks for the reply.
>
> For all-atom Amber ff, Should I change the neighbor list value or change in
> the cut-off for VdW interactions. As the side-chain hydrogen atoms might be
> clashing with the lipid atoms and thus producing many LINCS warning.
>
> Thanks
> Ram
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[gmx-users] output - em.gro looks very strange

[gmx-users] non-bonded potential

[gmx-users] g_sham experimental weighting with temperature

[gmx-users] Using custom potential for electrostatics between protein and water

Re: [gmx-users] Using custom potential for electrostatics between protein and water

Re: [gmx-users] Using custom potential for electrostatics between protein and water

[gmx-users] different pull force constants

Re: [gmx-users] Using custom potential for electrostatics between protein and water

Re: [gmx-users] How the index is recognised for values more than 99999?

[gmx-users] Unable to write whole trajectory with trjconv and error in gmx check

[gmx-users] RADIAL DISTRIBUTION FUNTION

Re: [gmx-users] Insertion of Ion-channels onto the membrane using g_membed with Amber force field

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