Re: [gmx-users] minimum distance between the protein and its mirror image

[OuyangYanhua]

The minimum protein-image distance is less than the value 2.0nm, such as t 
around 1.6nm above. Does it mean my simulation is failed in the box size set?
> 在 2016年8月29日，下午8:58，Justin Lemkul  写道：
> 
> 
> 
> On 8/29/16 5:02 AM, YanhuaOuyang wrote:
>> Hi,
>>   I am running a REMD of a disordered protein, I visualized the trajectory 
>> in VMD and I found that the protein is very close to the box edge.
>>   Then I use "gmx mindist " to  check  if a protein has seen its periodic 
>> image during simulation. When I used the command "gmx mindist -f remd_01.pdb 
>> -s remd.tpr -od mindist.xvg -pi" I choose the 1 group---protein. I choose 
>> some data from  mindist.xvg, they are as follow:
>>02.800  5.225  7.200  7.200  7.200
>>22.793  5.136  7.200  7.200  7.200
>>42.804  5.002  7.200  7.200  7.200
>>62.777  5.176  7.200  7.200  7.200
>>82.820  5.187  7.200  7.200  7.200
>>10   2.871  5.043  7.200  7.200  7.200
>>12   2.788  5.089  7.200  7.200  7.200
>>14   2.882  4.892  7.200  7.200  7.200
>>   
>>5154 4.153  3.415  7.200  7.200  7.200
>>5156 4.222  3.483  7.200  7.200  7.200
>>5158 4.154  3.608  7.200  7.200  7.200
>>5172 3.607  4.124  7.200  7.200  7.200
>>5174 3.556  4.140  7.200  7.200  7.200
>>5176 3.303  4.430  7.200  7.200  7.200
>>5178 3.291  4.297  7.200  7.200  7.200
>>...
>>5880 1.659  5.595  7.200  7.200  7.200
>>5882 1.787  5.564  7.200  7.200  7.200
>>5884 1.718  5.575  7.200  7.200  7.200
>>5886 1.669  5.654  7.200  7.200  7.200
>>5888 1.636  5.752  7.200  7.200  7.200
>>5890 1.590  5.761  7.200  7.200  7.200
>>5892 1.620  5.786  7.200  7.200  7.200
>>5894 1.513  5.791  7.200  7.200  7.200
>>5896 1.523  5.908  7.200  7.200  7.200
>> I set the short-range VDW and electrostatic cutoffs=1.0 nm, the distance 
>> between the outside of protein and the edge of box is 1.0 nm. the Minimum 
>> distance to periodic image ranges from 1.5 nm to 4.2 nm from the data above. 
>> While the deal value should be at least 2.0 nm, which is double the cutoff.
>> Do anyone knows the simulation is normal and if a protein has seen its 
>> periodic image during simulation?
> 
> It has not seen its periodic image with cutoffs = 1.0 nm.  You have a very 
> thin shell of water around the protein, though, which means there could be 
> some artificial ordering, but whether or not that's enough to seriously 
> perturb the dynamics is not immediately clear.
> 
>> which group should I choose when i using gmx mindist, protein, C-alpha or 
>> some else?
>> 
> 
> Protein.  You need to verify that all protein atoms behaved correctly.  CA 
> atoms are unlikely to ever see their own periodic images unless you have done 
> something horribly wrong in setting up your box.
> 
> -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: * of the *** bonded interactions could not be calculated because ...

[Chang Woon Jang]

Dear Gromacs Users,


I have a Fatal error as follow. The error says -rdd option or -ddcheck. How
can I properly use these options? Is the following command the proper use
of these options?

> gmx mdrun -s topol.tpr -c confout.gro -o traj.trr -x traj.xtc -rdd 1.5
-ddcheck

Thank you.


1 of the 1612 bonded interactions could not be calculated because some
atoms involved moved further apart than the multi-body cut-off distance
(1.5 nm) or the two-body cut-off distance (1.5 nm), see option -rdd, for
pairs and tabulated bonds also see option -ddcheck
For more information and tips for troubleshooting, please check the GROMACS




Best regards,
Changwoon Jang,
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Re: [gmx-users] Grace on Mac OS

[Daryl CHRZAN]

You might try homebrew: http://brewformulas.org/Grace.


Daryl C. Chrzan

Professor, Materials Science and Engineering
Vice Chair for Academic Affairs, Materials Science and Engineering
Chair, Applied Science and Technology
University of California
Berkeley, CA 94720

and

Faculty Staff Scientist
Materials Sciences Division
Lawrence Berkeley National Laboratory

ph: 510 643 1624
email: dcchr...@berkeley.edu

On Mon, Aug 29, 2016 at 2:51 PM, Soheil Fatehiboroujeni <
sfatehiborouj...@ucmerced.edu> wrote:

> Hi,
>
> I am trying to see .xvg plots in Mac OS 10.11.3, so that I can avoid
> ubuntu and save some time if possible. I follow this link:
> http://www.phy.ohiou.edu/~hadizade/MRHadizadeh/Blog/
> Entries/2013/8/5_Installing_XmGrace_(Grace)_on_Mac_OS_X.html
>
> but during the installation of "openmotif-compat-2.1.32_IST.macosx10.5.dmg”
> I receive this message that open motif is not compatible with my OS.
>
> I appreciate if someone can help with this? Or, is there an alternative
> way to get plots similar to the ones with “xmgrace" in ubuntu.
>
> Best,
>
> Soheil
>
>
>
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[gmx-users] Grace on Mac OS

[Soheil Fatehiboroujeni]

Hi,

I am trying to see .xvg plots in Mac OS 10.11.3, so that I can avoid ubuntu and 
save some time if possible. I follow this link: 
http://www.phy.ohiou.edu/~hadizade/MRHadizadeh/Blog/Entries/2013/8/5_Installing_XmGrace_(Grace)_on_Mac_OS_X.html

but during the installation of "openmotif-compat-2.1.32_IST.macosx10.5.dmg” I 
receive this message that open motif is not compatible with my OS.

I appreciate if someone can help with this? Or, is there an alternative way to 
get plots similar to the ones with “xmgrace" in ubuntu.

Best,

Soheil



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Re: [gmx-users] Fwd: tau-t effects on sd integrator

[Sidong Tu]

Thank you very much, Justin. I'll go and try with 2ps.


Best wishes,
Sidong

On Mon, Aug 29, 2016 at 1:38 PM, Justin Lemkul  wrote:

>
>
> On 8/29/16 1:29 PM, Sidong Tu wrote:
>
>> Dear all,
>>
>> I was trying to simulate lysozyme and polymer in water model tip3p using
>> charmm36 force field at 500K on Gromacs 5.1.2. The software ran on GPU and
>> the system size was about 60,000 atoms. I used sd as integrator and the
>> tau-t option was 0.1. I wondered if there is any problem with this option
>> for the suggested tau-t is 0.2 in manual. If is, how this influence the
>> result?
>>
>>
> I don't know where you see a recommendation of 0.2 as tau-t.  See
> http://manual.gromacs.org/documentation/5.1.2/user-guide/
> mdp-options.html#run-control
>
> "When used as a thermostat, an appropriate value for tau-t is 2 ps, since
> this results in a friction that is lower than the internal friction of
> water, while it is high enough to remove excess heat NOTE: temperature
> deviations decay twice as fast as with a Berendsen thermostat with the same
> tau-t."
>
> With a very low tau-t and SD, you probably have strongly over-damped
> dynamics.
>
> -Justin
>
> Here is my full .mdp file:
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> *title= protein in watercpp  =
>> /lib/cpp;define  = -DPOSRES; RUN
>> CONTROLintegrator   = sdnsteps   =
>> 1dt   = 0.002; NEIGHBOR
>> SEARCHINGnstlist  = 50cutoff-scheme=
>> verletns_type  = gridpbc  =
>> xyzrlist= 1.2; OUTPUT CONTROLnstxout
>> =
>> 0nstvout  = 0nstxtcout=
>> 5000nstlog   = 5000constraints  =
>> h-bondsconstraint_algorithm = LINCSlincs-iter   =
>> 1lincs-order  = 6nstenergy=
>> 5000continuation = yes; OPTION FOR ELECTROSTATIC AND
>> VDWcoulombtype  = PMErcoulomb_switch  =
>> 0rcoulomb = 1.2; Dielectric constant (DC) for cut-off or
>> DC
>> of reaction fieldepsilon_r= 1; Method for doing Van der
>> Waalsvdw-type = Cut-offvdw-modifier =
>> force-switch; cut-off lengthsrvdw_switch  =
>> 1.00rvdw = 1.20; Apply long range dispersion
>> corrections for Energy and PressureDispCorr = No;
>> Extension
>> of the potential lookup tables beyond the cut-offtable-extension
>> =
>> 2.5; Spacing for the PME/PPPM FFT gridfourierspacing   = 0.12; FFT
>> grid size, when a value is 0 fourierspacing will be
>> usedfourier_nx   = 0fourier_ny   =
>> 0fourier_nz   = 0; EWALD/PME/PPPM
>> parameterspme_order= 4ewald_rtol   =
>> 1e-05ewald_geometry   = 3depsilon_surface  =
>> 0optimize_fft = no; OPTIONS FOR WEAK COUPLING
>> ALGORITHMStcoupl   = v-rescaletc_grps  =
>> Protein_NAG Water_and_ions Polymertau_t= 0.1 0.1
>> 0.1ref_t= 500 500  500Pcoupl   =
>> Parrinello-Rahmanpcoupltype   = isotropic; Time
>> constant (ps), compressibility (1/bar) and reference P
>> (bar)tau_p= 2.0compressibility  =
>> 4.5e-5ref_p= 1.0refcoord_scaling =
>> comgen_vel  = nogen_temp = 500; OPTIONS
>> FOR
>> LANGEVIN DYNAMICSld-seed  = -1*
>> Best wishes,
>> Sidong
>>
>>
> --
> ==
>
> 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] QM/MM simulations

[Mark Abraham]

Hi,

Sadly, most of the QM/MM interfaces have been lacking a maintainer on the
GROMACS side for quite a number of years. You should definitely be
following http://wwwuser.gwdg.de/~ggroenh/qmmm.html closely.

Mark

On Mon, Aug 29, 2016 at 9:36 PM Clinton King 
wrote:

> I'm performing a QM/MM (using Gaussian 09 and Gromacs 5.1.2) simulation of
> a single molecule of octanol in a box of water. In examining the standard
> output, it appears that call to Gaussian is proceeding as expected, but
> looking at the log file, it doesn't appear that quantum energy is being
> communicated correctly, ie the output looks like the following:
>
>
>
>Step   Time Lambda
>70007.00.0
>
>Energies (kJ/mol)
> LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>  Quantum En.
> 2.45033e+04   -1.74106e+02   -1.86935e+056.68753e+010.0e+00
>   Potential  Kinetic En. Total EnergyTemperature
>  Pres. DC (bar)
>-1.62539e+053.00966e+04   -1.32443e+052.97582e+02   -2.34549e+01
>  Pressure (bar)   Constr. rmsd
>-7.37300e+018.07450e-06
>
>
> Notice that the entry for Quantum En. is 0.000.
>
> Has anyone else seen this problem before? If so, what did you do about it?
>
> --
> Clinton King
> Graduate Student
> Chemistry Department
> Brigham Young University
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[gmx-users] QM/MM simulations

[Clinton King]

I'm performing a QM/MM (using Gaussian 09 and Gromacs 5.1.2) simulation of
a single molecule of octanol in a box of water. In examining the standard
output, it appears that call to Gaussian is proceeding as expected, but
looking at the log file, it doesn't appear that quantum energy is being
communicated correctly, ie the output looks like the following:



   Step   Time Lambda
   70007.00.0

   Energies (kJ/mol)
LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
 Quantum En.
2.45033e+04   -1.74106e+02   -1.86935e+056.68753e+010.0e+00
  Potential  Kinetic En. Total EnergyTemperature
 Pres. DC (bar)
   -1.62539e+053.00966e+04   -1.32443e+052.97582e+02   -2.34549e+01
 Pressure (bar)   Constr. rmsd
   -7.37300e+018.07450e-06


Notice that the entry for Quantum En. is 0.000.

Has anyone else seen this problem before? If so, what did you do about it?

--
Clinton King
Graduate Student
Chemistry Department
Brigham Young University
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[gmx-users] evaluation of influence of pH on the stability of protein

[Mahboobeh Eslami]

 Hi all Gmx usersI want to evaluate influence of pH on the stability of  
protein.  can I use MD simulation for this goal? thanks




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Re: [gmx-users] Fwd: tau-t effects on sd integrator

[Justin Lemkul]

On 8/29/16 1:29 PM, Sidong Tu wrote:

Dear all,

I was trying to simulate lysozyme and polymer in water model tip3p using
charmm36 force field at 500K on Gromacs 5.1.2. The software ran on GPU and
the system size was about 60,000 atoms. I used sd as integrator and the
tau-t option was 0.1. I wondered if there is any problem with this option
for the suggested tau-t is 0.2 in manual. If is, how this influence the
result?



I don't know where you see a recommendation of 0.2 as tau-t.  See 
http://manual.gromacs.org/documentation/5.1.2/user-guide/mdp-options.html#run-control


"When used as a thermostat, an appropriate value for tau-t is 2 ps, since this 
results in a friction that is lower than the internal friction of water, while 
it is high enough to remove excess heat NOTE: temperature deviations decay twice 
as fast as with a Berendsen thermostat with the same tau-t."


With a very low tau-t and SD, you probably have strongly over-damped dynamics.

-Justin


Here is my full .mdp file:






































































*title= protein in watercpp  =
/lib/cpp;define  = -DPOSRES; RUN
CONTROLintegrator   = sdnsteps   =
1dt   = 0.002; NEIGHBOR
SEARCHINGnstlist  = 50cutoff-scheme=
verletns_type  = gridpbc  =
xyzrlist= 1.2; OUTPUT CONTROLnstxout  =
0nstvout  = 0nstxtcout=
5000nstlog   = 5000constraints  =
h-bondsconstraint_algorithm = LINCSlincs-iter   =
1lincs-order  = 6nstenergy=
5000continuation = yes; OPTION FOR ELECTROSTATIC AND
VDWcoulombtype  = PMErcoulomb_switch  =
0rcoulomb = 1.2; Dielectric constant (DC) for cut-off or DC
of reaction fieldepsilon_r= 1; Method for doing Van der
Waalsvdw-type = Cut-offvdw-modifier =
force-switch; cut-off lengthsrvdw_switch  =
1.00rvdw = 1.20; Apply long range dispersion
corrections for Energy and PressureDispCorr = No; Extension
of the potential lookup tables beyond the cut-offtable-extension  =
2.5; Spacing for the PME/PPPM FFT gridfourierspacing   = 0.12; FFT
grid size, when a value is 0 fourierspacing will be
usedfourier_nx   = 0fourier_ny   =
0fourier_nz   = 0; EWALD/PME/PPPM
parameterspme_order= 4ewald_rtol   =
1e-05ewald_geometry   = 3depsilon_surface  =
0optimize_fft = no; OPTIONS FOR WEAK COUPLING
ALGORITHMStcoupl   = v-rescaletc_grps  =
Protein_NAG Water_and_ions Polymertau_t= 0.1 0.1
0.1ref_t= 500 500  500Pcoupl   =
Parrinello-Rahmanpcoupltype   = isotropic; Time
constant (ps), compressibility (1/bar) and reference P
(bar)tau_p= 2.0compressibility  =
4.5e-5ref_p= 1.0refcoord_scaling =
comgen_vel  = nogen_temp = 500; OPTIONS FOR
LANGEVIN DYNAMICSld-seed  = -1*
Best wishes,
Sidong



--
==

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] Fwd: tau-t effects on sd integrator

[Sidong Tu]

Dear all,

I was trying to simulate lysozyme and polymer in water model tip3p using
charmm36 force field at 500K on Gromacs 5.1.2. The software ran on GPU and
the system size was about 60,000 atoms. I used sd as integrator and the
tau-t option was 0.1. I wondered if there is any problem with this option
for the suggested tau-t is 0.2 in manual. If is, how this influence the
result?

Here is my full .mdp file:






































































*title= protein in watercpp  =
/lib/cpp;define  = -DPOSRES; RUN
CONTROLintegrator   = sdnsteps   =
1dt   = 0.002; NEIGHBOR
SEARCHINGnstlist  = 50cutoff-scheme=
verletns_type  = gridpbc  =
xyzrlist= 1.2; OUTPUT CONTROLnstxout  =
0nstvout  = 0nstxtcout=
5000nstlog   = 5000constraints  =
h-bondsconstraint_algorithm = LINCSlincs-iter   =
1lincs-order  = 6nstenergy=
5000continuation = yes; OPTION FOR ELECTROSTATIC AND
VDWcoulombtype  = PMErcoulomb_switch  =
0rcoulomb = 1.2; Dielectric constant (DC) for cut-off or DC
of reaction fieldepsilon_r= 1; Method for doing Van der
Waalsvdw-type = Cut-offvdw-modifier =
force-switch; cut-off lengthsrvdw_switch  =
1.00rvdw = 1.20; Apply long range dispersion
corrections for Energy and PressureDispCorr = No; Extension
of the potential lookup tables beyond the cut-offtable-extension  =
2.5; Spacing for the PME/PPPM FFT gridfourierspacing   = 0.12; FFT
grid size, when a value is 0 fourierspacing will be
usedfourier_nx   = 0fourier_ny   =
0fourier_nz   = 0; EWALD/PME/PPPM
parameterspme_order= 4ewald_rtol   =
1e-05ewald_geometry   = 3depsilon_surface  =
0optimize_fft = no; OPTIONS FOR WEAK COUPLING
ALGORITHMStcoupl   = v-rescaletc_grps  =
Protein_NAG Water_and_ions Polymertau_t= 0.1 0.1
0.1ref_t= 500 500  500Pcoupl   =
Parrinello-Rahmanpcoupltype   = isotropic; Time
constant (ps), compressibility (1/bar) and reference P
(bar)tau_p= 2.0compressibility  =
4.5e-5ref_p= 1.0refcoord_scaling =
comgen_vel  = nogen_temp = 500; OPTIONS FOR
LANGEVIN DYNAMICSld-seed  = -1*
Best wishes,
Sidong
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[gmx-users] calculation of pKa

[Rui Neves]

Dear Gromacs users,

I am trying to perform a pKa calculation of a Cys in a thioredoxin-protein
(Trx) using the FEP implementation of Gromacs 5.1.0.

I am transforming the charge in CYS to that of a CYM in 10 equally-spaced
lambda steps, and then turning off the vdw radii of the hydrogen (HS) in
the thiol terminus of Cys in 20 equally-spaced lambda steps.

I have had no problems concerning the anhilation and redistribution of
charge in Cys.
However, I have had some problems with the anhilation of the vdw radii of
HS.
In this process I turn a HS into a dummy (DU) with no LJ energy of
interaction.
During the BAR analysis with the gmx bar program, I frequently come across
this warning:

*WARNING: Some of these results violate the Second Law of Thermodynamics: *
* This is can be the result of severe undersampling, or (more
likely)*
* there is something wrong with the simulations.*

I have tried to read about this in forums. I often read that it is related
to a negative entropy for states A and B to 'interact' with one another,
but there is no simple answer to solve this problem.

I have revised my mdp settings and have managed to solve the issue for the
case of the system comprising only Cys; however, I still cannot solve this
issue for the Trx system.
I tried to extend the simulation from 1 ns to 4 ns/lambda, but I keep
getting the same warning (I attach the bar plot to this mail).

*Temperature: 300 K*

*Detailed results in kT (see help for explanation):*

* lam_A  lam_BDG +/-   s_A +/-   s_B +/-
stdev +/- *
*10 11   -0.0359  0.00050.0060  0.00180.0070  0.0018
 0.1060  0.0006*
*11 12   -0.0427  0.00040.0120  0.00100.0130  0.0010
 0.1103  0.0007*
*12 13   -0.0414  0.00070.0003  0.00050.0012  0.0006
 0.1032  0.0007*
*13 14   -0.0384  0.00080.0080  0.00050.0087  0.0005
 0.0986  0.0008*
*14 15   -0.0394  0.00040.0053  0.00050.0059  0.0005
 0.0959  0.0004*
*15 16   -0.0322  0.0009   -0.0004  0.0007   -0.0001  0.0007
 0.0834  0.0007*
*16 17   -0.0267  0.00040.0046  0.00090.0047  0.0009
 0.0708  0.0002*
*17 18   -0.0214  0.0011   -0.0002  0.0012   -0.0001  0.0012
 0.0598  0.0006*
*18 19   -0.0162  0.00030.0025  0.00160.0026  0.0016
 0.0510  0.0006*
*19 20   -0.0124  0.00060.0007  0.00100.0008  0.0010
 0.0424  0.0004*
*20 21   -0.0094  0.00060.0022  0.00070.0022  0.0007
 0.0360  0.0004*
*21 22   -0.0046  0.0007   -0.0014  0.0003   -0.0014  0.0003
 0.0300  0.0004*
*22 230.0010  0.0005   -0.0002  0.0007   -0.0002  0.0007
 0.0239  0.0002*
*23 250.0083  0.00120.0031  0.00070.0019  0.0004
 0.0364  0.0002*
*25 260.0071  0.00030.0002  0.00020.0003  0.0004
 0.0138  0.0001*
*26 270.0093  0.0002   -0.0004  0.0002   -0.0004  0.0002
 0.0109  0.0001*
*27 280.0115  0.0001   -0.0002  0.0002   -0.0002  0.0002
 0.0090  0.0001*
*28 290.0126  0.00010.0004  0.00020.0004  0.0001
 0.0077  0.0001*
*29 300.0130  0.00010.0004  0.0.0004  0.
 0.0065  0.*

*WARNING: Some of these results violate the Second Law of Thermodynamics: *
* This is can be the result of severe undersampling, or (more
likely)*
* there is something wrong with the simulations.*


*Final results in kJ/mol:*

*point 10 - 11,   DG -0.0895 +/-  0.0013*
*point 11 - 12,   DG -0.1066 +/-  0.0010*
*point 12 - 13,   DG -0.1032 +/-  0.0019*
*point 13 - 14,   DG -0.0959 +/-  0.0019*
*point 14 - 15,   DG -0.0983 +/-  0.0009*
*point 15 - 16,   DG -0.0802 +/-  0.0022*
*point 16 - 17,   DG -0.0666 +/-  0.0010*
*point 17 - 18,   DG -0.0533 +/-  0.0028*
*point 18 - 19,   DG -0.0403 +/-  0.0007*
*point 19 - 20,   DG -0.0309 +/-  0.0014*
*point 20 - 21,   DG -0.0235 +/-  0.0016*
*point 21 - 22,   DG -0.0115 +/-  0.0017*
*point 22 - 23,   DG  0.0025 +/-  0.0013*
*point 23 - 25,   DG  0.0206 +/-  0.0031*
*point 25 - 26,   DG  0.0176 +/-  0.0008*
*point 26 - 27,   DG  0.0232 +/-  0.0004*
*point 27 - 28,   DG  0.0288 +/-  0.0002*
*point 28 - 29,   DG  0.0314 +/-  0.0002*
*point 29 - 30,   DG  0.0325 +/-  0.0001*

*total 10 - 30,   DG -0.6432 +/-  0.0037*

I have also analysed different timeblocks of the simulation, to no avail.
I have also tested the inclusion of the couple-moltype keyword, but the
problem remains. I get different free-energy estimates though. Does anyone
know what exactly means the couple-moltype keyword?

My mdp settings are as follow:


*; Run control*
*integrator   = sd   ; Langevin dynamics*
*tinit= 0*
*dt   = 0.002*
*nsteps   = 200   ; 4 ns*
*nstcomm  = 100*
*comm-mode   

Re: [gmx-users] Segmentation fault

[Justin Lemkul]

Please make sure to use a proper subject line and do not reply to the entire 
digest.

On 8/29/16 6:16 AM, Seera Suryanarayana wrote:

Sub: Segmentation fault

Dear Justin and Vivek,

I came to know what was my fault. I added the refcoordscale = com  in .mdp
file and it going fine. I have through the many references for
refcoordscale, despite of some information I am not getting what exactly it
is?  Kindly give me some hit.



The pressure coupling scaling matrix adjusts atomic positions in response to 
variations in pressure.  If you use a fixed reference as the origin of the 
position restraints, you will get a systematic drift in that position with 
respect to the coordinates propagated during dynamics.  So with the 
refcoord_scaling option, the reference coordinates (e.g. those at t=0, usually) 
have the same scaling matrix applied to them so that you don't get spurious 
contributions that might distort the structure.  The "com" option scales 
relative to the center-of-mass of the restrained group(s), whereas "all" scales 
every atom individually.  I find "com" to generally be the best option.


-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] minimum distance between the protein and its mirror image

[Justin Lemkul]

On 8/29/16 5:02 AM, YanhuaOuyang wrote:

Hi,
   I am running a REMD of a disordered protein, I visualized the trajectory in 
VMD and I found that the protein is very close to the box edge.
   Then I use "gmx mindist " to  check  if a protein has seen its periodic image during 
simulation. When I used the command "gmx mindist -f remd_01.pdb -s remd.tpr -od mindist.xvg 
-pi" I choose the 1 group---protein. I choose some data from  mindist.xvg, they are as follow:
02.800  5.225  7.200  7.200  7.200
22.793  5.136  7.200  7.200  7.200
42.804  5.002  7.200  7.200  7.200
62.777  5.176  7.200  7.200  7.200
82.820  5.187  7.200  7.200  7.200
10   2.871  5.043  7.200  7.200  7.200
12   2.788  5.089  7.200  7.200  7.200
14   2.882  4.892  7.200  7.200  7.200
   
5154 4.153  3.415  7.200  7.200  7.200
5156 4.222  3.483  7.200  7.200  7.200
5158 4.154  3.608  7.200  7.200  7.200
5172 3.607  4.124  7.200  7.200  7.200
5174 3.556  4.140  7.200  7.200  7.200
5176 3.303  4.430  7.200  7.200  7.200
5178 3.291  4.297  7.200  7.200  7.200
...
5880 1.659  5.595  7.200  7.200  7.200
5882 1.787  5.564  7.200  7.200  7.200
5884 1.718  5.575  7.200  7.200  7.200
5886 1.669  5.654  7.200  7.200  7.200
5888 1.636  5.752  7.200  7.200  7.200
5890 1.590  5.761  7.200  7.200  7.200
5892 1.620  5.786  7.200  7.200  7.200
5894 1.513  5.791  7.200  7.200  7.200
5896 1.523  5.908  7.200  7.200  7.200
I set the short-range VDW and electrostatic cutoffs=1.0 nm, the distance 
between the outside of protein and the edge of box is 1.0 nm. the Minimum 
distance to periodic image ranges from 1.5 nm to 4.2 nm from the data above. 
While the deal value should be at least 2.0 nm, which is double the cutoff.
Do anyone knows the simulation is normal and if a protein has seen its periodic 
image during simulation?


It has not seen its periodic image with cutoffs = 1.0 nm.  You have a very thin 
shell of water around the protein, though, which means there could be some 
artificial ordering, but whether or not that's enough to seriously perturb the 
dynamics is not immediately clear.



which group should I choose when i using gmx mindist, protein, C-alpha or some 
else?



Protein.  You need to verify that all protein atoms behaved correctly.  CA atoms 
are unlikely to ever see their own periodic images unless you have done 
something horribly wrong in setting up your box.


-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] Mass Weighted Covariance matrix

[Justin Lemkul]

On 8/29/16 12:16 AM, Tushar Modi wrote:

Hello

I am trying to calculate mass weighted covariance matrix using a Gromacs
Topology file  and a trajectory file . The trajectory has only
protein coordinates.
 I am using "gmx_mpi covar" function for the same. I am using following
format from the documentation:

gmx_mpi covar -f  -s  -ascii -mwa -b <> -e <>

I have tried it both with and without mwa, but in both cases the log file
generated says that the analysis is non mass weighted.
Does that mean that the covariance matrix is also non mass weighted or not??



Are the covariances matrices generated with and without explicit mass weighting 
different?  This could just be a simple output bug and nothing in the actual 
calculation.  What version of GROMACS are you using?


-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] KALP-15 tutorial

[Justin Lemkul]

On 8/28/16 11:13 AM, Roshan Shrestha wrote:

Actually, I thought that I made an error by minimizing system.gro instead
of system_inflated.gro. So, I ran energy minimization for
system_inflated.gro by renaming tutorial's minim.mdp as em.mdp-
gmx grompp -f em.mdp -c system_inflated.gro -p topol.top -o inflated_em1.tpr
But, I am again getting an error as-Warning: atom name 1 in topol.top and
system_inflated.gro does not match (C1 - CA)
Warning: atom name 2 in topol.top and system_inflated.gro does not match
(C2 - C)
Warning: atom name 3 in topol.top and system_inflated.gro does not match
(C3 - O)
Warning: atom name 4 in topol.top and system_inflated.gro does not match
(N4 - N)
Warning: atom name 5 in topol.top and system_inflated.gro does not match
(C5 - H)
Warning: atom name 6 in topol.top and system_inflated.gro does not match
(C6 - CA)
Warning: atom name 7 in topol.top and system_inflated.gro does not match
(O7 - C)
Warning: atom name 8 in topol.top and system_inflated.gro does not match
(P8 - O)
Warning: atom name 9 in topol.top and system_inflated.gro does not match
(O9 - N)
Warning: atom name 10 in topol.top and system_inflated.gro does not match
(O10 - H)
Warning: atom name 11 in topol.top and system_inflated.gro does not match
(O11 - CA)
Warning: atom name 12 in topol.top and system_inflated.gro does not match
(C12 - CB)
Warning: atom name 13 in topol.top and system_inflated.gro does not match
(C13 - CG)
Warning: atom name 14 in topol.top and system_inflated.gro does not match
(O14 - CD)
Warning: atom name 15 in topol.top and system_inflated.gro does not match
(C15 - CE)
Warning: atom name 16 in topol.top and system_inflated.gro does not match
(O16 - NZ)
Warning: atom name 17 in topol.top and system_inflated.gro does not match
(C17 - HZ1)
Warning: atom name 18 in topol.top and system_inflated.gro does not match
(C18 - HZ2)
Warning: atom name 19 in topol.top and system_inflated.gro does not match
(C19 - HZ3)
Warning: atom name 20 in topol.top and system_inflated.gro does not match
(C20 - C)
(more than 20 non-matching atom names)

WARNING 1 [file topol.top, line 930]:
  6438 non-matching atom names
  atom names from topol.top will be used
  atom names from system_inflated.gro will be ignored


Removing all charge groups because cutoff-scheme=Verlet
Analysing residue names:
There are:   126  Other residues
There are:17Protein residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting
into groups...
Analysing Protein...
Number of degrees of freedom in T-Coupling group rest is 19311.00
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 216x216x56, spacing 0.119 0.119 0.118
Estimate for the relative computational load of the PME mesh part: 0.96

NOTE 4 [file em.mdp]:
  The optimal PME mesh load for parallel simulations is below 0.5
  and for highly parallel simulations between 0.25 and 0.33,
  for higher performance, increase the cut-off and the PME grid spacing.


This run will generate roughly 1 Mb of data

There were 4 notes

There was 1 warning

---
Program gmx grompp, VERSION 5.1.3
Source code file:
/home/roshan/Downloads/gromacs-5.1.3/src/gromacs/gmxpreprocess/grompp.c,
line: 2107

Fatal error:
Too many warnings (1), gmx terminate
The end of my topol.top is-
 ; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif

; Strong position restraints for InflateGRO
#ifdef STRONG_POSRES
#include "strong_posre.itp"
#endif

; Include DPPC chain topology
#include "dppc.itp"

; Include water topology
#include "gromos53a6_lipid.ff/spc.itp"


#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct   fcxfcyfcz
   11   1000   1000   1000
#endif

; Include topology for ions
#include "gromos53a6_lipid.ff/ions.itp"

[ system ]
; Name
frame t= 1.000

[ molecules ]
; Compound#mols
DPPC126s
Protein 1

There are 17503 atoms in system.gro while only 6438 in system_inflated.gro.
Are the errors due to this difference ?



Your topology is out of order with respect to the coordinates.  Follow the 
tutorial exactly; it lays out what modifications to make.  Also note that "126s" 
is invalid and should just be the number 126.


The difference in system.gro and system_inflated.gro is that water has been 
deleted by InflateGRO.  It is supposed to do this.  Do not add any water to the 
system until it is done being packed, as instructed by the tutorial.


-Justin





On Sun, Aug 28, 2016 at 3:34 PM, Roshan Shrestha 
wrote:


After using this step-
*perl inflategro.pl  system.gro 4 DPPC 14
system_inflated.gro 5 area.dat*
Reading.
Scaling lipids
There are 128 lipids...
with 50 atoms per lipid..

Determining upper and lower leaflet...
64 lipids in the upper...
64 lipids in the lower leaflet

Centering protein
Checking for overlap
...this 

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 148, Issue 102

[Seera Suryanarayana]

Sub: Segmentation fault

Dear Justin and Vivek,

I came to know what was my fault. I added the refcoordscale = com  in .mdp
file and it going fine. I have through the many references for
refcoordscale, despite of some information I am not getting what exactly it
is?  Kindly give me some hit.

Surya
Graduate student
India.

On Sun, Aug 28, 2016 at 3:30 PM, <
gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote:

> Send gromacs.org_gmx-users mailing list submissions to
> gromacs.org_gmx-users@maillist.sys.kth.se
>
> To subscribe or unsubscribe via the World Wide Web, visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or, via email, send a message with subject or body 'help' to
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>
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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: Segmentation fault (Justin Lemkul)
>2. gmx: malloc(): memory corruption (Quyen V. Vu)
>3. KALP-15 tutorial (Roshan Shrestha)
>
>
> --
>
> Message: 1
> Date: Sat, 27 Aug 2016 22:17:13 -0400
> From: Justin Lemkul 
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Segmentation fault
> Message-ID: <960b62bc-d72d-9ad7-4625-e2c279df5...@vt.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> On 8/27/16 5:32 PM, vivek naik wrote:
> > I don't think you can do a simulation with pressure if you have position
> > restraints, except if your restrained atoms are all in the same plane.
>
> This is not true.
>
> > However, ref_coordscaling option should be 'com', which should make it
> > better than it is now.
> >
>
> "com" is just one possible option, but it is probably the most stable in
> most cases.
>
> > Also, there is no way isotropic pressure is going to work. it has to be
> > anisotropic (xy and z, with the first one being kept to zero).
> >
>
> Anisotropic means all box vectors can vary independently and is usually
> applied
> to crystals or other solid materials.  Coupling xy and z separately is
> semiisotropic and is usually used with membranes and surfaces.  For a
> simple
> aqueous protein system, isotropic is in fact correct.
>
> -Justin
>
> > Vivek
> >
> > On Sat, Aug 27, 2016 at 12:15 PM, Seera Suryanarayana <
> paluso...@gmail.com>
> > wrote:
> >
> >> Dear gromacs users,
> >>
> >> I have done mdrun for 10ns with position restrain of interest of our
> >> residues. Here I woulk like to explain how I did the position restrain.
> >>
> >> During gmx pdb2gmx command we usually get posre.itp file which we use in
> >> the equilibrium process to restraint the protein. As I want to do real
> >> mdrun with restraint on some residues, I just edited the posre.itp file
> and
> >> kept the restrain information only for residues of my interest and I
> define
> >> in the md.mdp file as "define  =_DPOSRES   ; position restrain the
> >> protein".  I haven't anything to the topology file. When I executed the
> >> grompp command I got following warning and then error.
> >>
> >> WARNING 1 [file md.mdp]:
> >> you are using pressure coupling with absolute positions restraints, this
> >> will give artifacts. use the refcoord_scaling option and the error was
> too
> >> many wanrings[1], gmx terminated. Then I executed grompp with the
> -maxwarn
> >> 1. After preprocessing  I did simuations for 10ns. When I try to remove
> the
> >> PBC with trjconv command I got segmentaion fault error. I request you to
> >> tell me What I did wrong and how to resolve it?
> >>
> >> Thanks in advance
> >> Surya
> >> Graduate student
> >> India.
> >> --
> >> 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.
> >>
> >
> >
> >
>
> --
> ==
>
> 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: Sun, 28 Aug 2016 14:47:30 +0700
> From: "Quyen V. Vu" 
> To: "gromacs.org_gmx-users@maillist.sys.kth.se"
> 
> Subject: [gmx-users] gmx: 

Re: [gmx-users] Finding Average Net charge as a function of distance from a polymer segment

[Abhishek Gupta]

Dear Gromacs Users

I want to examine the distribution of counterions in my system at larger
length scales comparable to the size of the molecule. I have used RDF's to
find the distribution of ions till half the box size. Can I consider half
the box size as larger length scale ?
I have found in a paper that ion distribution surrounding the polymer can
be calculated without normalizing by the volume of the spherical shell via
average net charge calculation for diffuse counterions in my system.
My question is How can I find the average net charge as a function of
distance from the polymer segement for a polymer chain using GROMACS 4.0.7
?
My system contains a single polymer chain, counterions and mixed solvent.

I will be grateful for the solution of the above issue.

Regards
-- 
Abhishek Kumar Gupta
Research Scholar
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[gmx-users] minimum distance between the protein and its mirror image

[YanhuaOuyang]

Hi,
   I am running a REMD of a disordered protein, I visualized the trajectory in 
VMD and I found that the protein is very close to the box edge.
   Then I use "gmx mindist " to  check  if a protein has seen its periodic 
image during simulation. When I used the command "gmx mindist -f remd_01.pdb -s 
remd.tpr -od mindist.xvg -pi" I choose the 1 group---protein. I choose some 
data from  mindist.xvg, they are as follow:
02.800  5.225  7.200  7.200  7.200
22.793  5.136  7.200  7.200  7.200
42.804  5.002  7.200  7.200  7.200
62.777  5.176  7.200  7.200  7.200
82.820  5.187  7.200  7.200  7.200
10   2.871  5.043  7.200  7.200  7.200
12   2.788  5.089  7.200  7.200  7.200
14   2.882  4.892  7.200  7.200  7.200
   
5154 4.153  3.415  7.200  7.200  7.200
5156 4.222  3.483  7.200  7.200  7.200
5158 4.154  3.608  7.200  7.200  7.200
5172 3.607  4.124  7.200  7.200  7.200
5174 3.556  4.140  7.200  7.200  7.200
5176 3.303  4.430  7.200  7.200  7.200
5178 3.291  4.297  7.200  7.200  7.200
...
5880 1.659  5.595  7.200  7.200  7.200
5882 1.787  5.564  7.200  7.200  7.200
5884 1.718  5.575  7.200  7.200  7.200
5886 1.669  5.654  7.200  7.200  7.200
5888 1.636  5.752  7.200  7.200  7.200
5890 1.590  5.761  7.200  7.200  7.200
5892 1.620  5.786  7.200  7.200  7.200
5894 1.513  5.791  7.200  7.200  7.200
5896 1.523  5.908  7.200  7.200  7.200
I set the short-range VDW and electrostatic cutoffs=1.0 nm, the distance 
between the outside of protein and the edge of box is 1.0 nm. the Minimum 
distance to periodic image ranges from 1.5 nm to 4.2 nm from the data above. 
While the deal value should be at least 2.0 nm, which is double the cutoff.
Do anyone knows the simulation is normal and if a protein has seen its periodic 
image during simulation?
which group should I choose when i using gmx mindist, protein, C-alpha or some 
else?

Best regards,
Ouyang
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