[gmx-users] Question regarding g_order
Hi all, I am trying to compute the order parameters for the sn1 and sn2 chains of DOPC (CHARMM36) in bilayer . I am using the g_order tool (v4.6.3). I have constructed for each DOPC chain two index files that contains in the first one all the Carbon atoms where the first Carbon is C=O and the last one is the last methyl. The second index file for the unsat calculations contains only the carbons of the C-C9=C10-C. I am confused here, since the file obtained from g_order w/o the -unsat argument contains only 16 values and in case of the file generated with g_order w the -unsat argument 2 values. I am aware that I need to replace the 9 -10 values in first by those of the second file. However I would like to compare my SCD values with those obtained by Jämbeck and P. Lyubartsev (figure 2 in ref [1] ), The authors present graph for DOPC with 17 values. How it is possible? Did I miss something, here? -- g_order w/o unsat # g_order_mpi is part of G R O M A C S: # # GROup of MAchos and Cynical Suckers # @title Deuterium order parameters @xaxis label Atom @yaxis label Scd @TYPE xy 10.20508 2 0.148241 3 0.184247 4 0.184565 5 0.184457 6 0.166101 7 0.118359 8 0.0774722 9 0.0703466 10 0.0511651 11 0.0977673 12 0.0968413 13 0.100903 14 0.0869513 15 0.0806322 16 0.0602708 -- g_order w/ unsat # g_order_mpi is part of G R O M A C S: # # GRoups of Organic Molecules in ACtion for Science # @title Deuterium order parameters @xaxis label Atom @yaxis label Scd @TYPE xy 1 0.104554 2 0.0111027 [1] http://pubs.acs.org/doi/full/10.1021/ct300342n Thank in advance -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Problems with simulations of a triclinic crystal lattice with Parrinello-Rahman
Hello everybody, I am trying to simulate a triclinic cristal lattice (4x4x2) with gromacs (4.5.5) in constant pressure with the Parrinello-Rahman (PR) barostat. the crystal were previously equilibrated in the NPT ensemble during 1ns at 200K with berendsen thermostat/barostat . The crystal initail parameters are (28.736 32.292 34.142 91.04 93.50 110.06 P 1) I used the following parameters . Tcoupl = v-rescale tc-grps = BCL BEN tau-t = 0.1 0.1 ref-t = 200 200 ; Pressure coupling is on Pcoupl = Parrinello-Rahman pcoupltype = isotropic tau_p = 5.0 compressibility = 4.5e-5 ref_p = 1.0135 gen_vel = no DispCorr= EnerPres . With these parameters, the system explodes. I am confused here because if I switch to the berendsen barostat with the following parameters I have no problems to do a simulation of 1ns and the crystal lattice parameters remains stable (see below) . isotropic Tcoupl = v-rescale tc-grps = BCL BEN tau-t = 0.1 0.1 ref-t = 200 200 ; Pressure coupling is on Pcoupl = berendsen pcoupltype = isotropic tau_p = 2.0 compressibility = 4.5e-5 ref_p = 1.0135 gen_vel = no DispCorr= EnerPres . Energy Average Err.Est. RMSD Tot-Drift --- Temperature 199.576 0.0233.56331 0.0876693 (K) Pressure 1.0242 0.25971.331 -0.346972 (bar) Box-X 2.914645.7e-05 0.00129697 6.17829e-05 (nm) Box-Y 3.07662 6e-05 0.00136905 6.52159e-05 (nm) Box-Z3.45356.7e-05 0.00153675 7.3165e-05 (nm) Volume 30.9685 0.0018 0.0413433 0.00197128 (nm^3) T-BCL 199.516 0.023.83149 0.0860062 (K) T-BEN 199.981 0.0489.94395 0.0989034 (K) CRYST1 29.137 32.742 34.618 91.04 93.50 110.06 P 1 Did I miss something important here about PR and crystals? SA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] How to compute the C-H bond time correlation function for surfactant alkyl chain in micelle with the CHARMM and GROMOS
Hi All, I would like to compute the time correlation function (tcf) of the C-H bond vector for all the C-H bonds on the hydrocarbon chain of surfactants in two micelles simulated with the CHARMM and gromos54A7 force fields. It is not clear to me how do that. Below what i did 1- For the CHARMM simulation I have constructed an index file that contains all the C H atoms of the alkyl chain, like this : aC12 | aH12A | aH12B aC13 | aH13A | aH13B ... ... ... up to the last methylene group aC23| aH23A | aH23B It is Correct ? 2- And use the following command for example for the C12-H bond vector g_rotacf_mpi -f micelle_Center_All.xtc -s run_1.tpr -b 11 -e 13 -fitfn aexp -d -n micelle_CH_Bonds.ndx -o micelle_rotacf-C12-P2.xvg bond_C12.txt It is also Correct ? I have indeed obtained a correlation function C(t), that i can fit with 4 exponential but i am not sure if this function is what i expect. IF It is ok, i would like to do the same calculations for surfactants simulated with GROMOS force field. Since in this force field the apolar hydrogens are not presents, i need to reconstruct them from hydrocarbon chain backbone. Again how to do that ? Your guidance would be helpful for me. Best SA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Question about the translational diffusion
Hi all, : A quick question here: Does the g_msd program (v4.5.5) take into account the finite size effect due to PBC when it computes/gives translational diffusion ? sa -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Conversion of the GLYCAM dihedral parameters
Thank you Olivier for your response.
SA
--
Message: 2
Date: Thu, 28 Jul 2011 11:20:44 +0100
From: Oliver Grant olivercgr...@gmail.com
Subject: Re: [gmx-users] Conversion of the GLYCAM dihedral parameters
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID:
CAFd05fG5yAzPHr=ssficaa0ff0q7uet3ib_yjrs70qme3n3...@mail.gmail.com
Content-Type: text/plain; charset=windows-1252
Hi SA,
I think this is due to the original amb2gmx.pl coder only considering
AMBER
type dihedrals. He/She didn't expect any negative values. You'll notice
certain groups like NAc and COO- on sugars are affected when you run your
simulation. Below is a similar post with a fix to the amb2gmx.pl code.
It's
short so I pasted it rather than linking.
You may already know this but note also the default is to correctly fudge
AMBERS 1-4 interactions. So if you run a sugar using the GLYCAM forcefield
they will be incorrectly scaled/fudged. An easy fix is to copy the
ffamber99sb.itp (may be called something else now) to your local directory
where you are running the md and change to:
[ defaults ]
; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ
1 2 yes 1.0
1.0
If you have a sugar and a protein you cannot mix the scaling. Mixed scaling
is possible in amber11 if you really need it. I did all this when 4.0.7 was
the latest release so things may have changed and it may now be possible to
mix scaling or it may be that something else has changed :)
If you find anything when testing the parameters please do post back.
All the best,
Oliver
*Hi all,
There is a problem that I encountered when I was trying to manually
verify the proper dihedral conversion from AMBER topology to GROMACS
topology using amb2gmx perl script.
Some of the dihedrals were set to zero by amb2gmx even if in the
prmtop file they were not zero. This was happening for all the lines
that had PK with negative values!. Reading the script I came up with
the following lines for V[i] calculation (lines 749 to 755 in the
script file):
...
# get all force constants for each line of a dihedral #
my $lines = $i -1 +$numijkl;
for(my $j=$i;$j=$lines;$j++){
my $period = abs($pn{$j});
if($pk{$j}0) {
$V[$period] = 2*$pk{$j}*$cal/$idivf{$j};
}
...
It seems from here that only PK values 0 are considered when
computing the RB constants.
After I change the sign to != (i.e. not equal to) everything
goes fine and ALL the dihedral are transformed correctly.
While this is OK with different AMBER sets and GAFF if one wish to
convert a GLYCAM (which comes also with Amber package) generated
topology, in the gromacs resultant file there will be missing
parameters for dihedrals. That's because GLYCAM does not use phase
shift and have also negative values for several PK
Is this a bug or there is a reason for considering only the positive
values of PK or I am missing something (as I am a begginer with
AMBER)?
(or maybe amb2gmx was designed only to work an AMBER ff conversion and
not for example GLYCAM)
Thanks for any comment,
Andrei*
On 21 July 2011 10:48, sa sagmx.m...@gmail.com wrote:
Yeah I have also found this page. Finally I did the conversion. I am
currently testing the parameters.
Thank you Austin and Mark for your help
SA-
--
Message: 4
Date: Wed, 20 Jul 2011 07:17:18 -0700 (PDT)
From: Austin B. Yongye ybau...@yahoo.com
Subject: Re: [gmx-users] Conversion of the GLYCAM dihedral parameters
in the GROMACS format.
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID:
1311171438.14853.yahoomailclas...@web161422.mail.bf1.yahoo.com
Content-Type: text/plain; charset=utf-8
So my questions are: how to convert it in the gromacs format ?
I haven't done AMBER to GROMACS conversions. But a google search led me
to
this page. It's just a matter of knowing the different formats.
http://ffamber.cnsm.csulb.edu
Is it correct to use the absolute value of the multiplicity in my
parameters and use the negative values of barrier heights when they are
exist in the AMBER parameters? Since, I have noticed that in the AMBER
ff port in GROMACS, the multiplicity values are always set to 0
and the barrier heights have sometime a negative value.
So my questions are: how to convert it in the gromacs format ? Is it
correct to use the absolute value of the multiplicity in my parameters
and
use the negative values of barrier heights when they are exist in the
AMBER
parameters? Since, I have noticed that in the AMBER ff port in GROMACS,
the
multiplicity values are always set to 0 and the barrier heights have
sometime a negative value.
Thank you again for your advice.
SA-
Message: 1
Date
[gmx-users] Conversion of the GLYCAM dihedral parameters
Yeah I have also found this page. Finally I did the conversion. I am currently testing the parameters. Thank you Austin and Mark for your help SA- -- Message: 4 Date: Wed, 20 Jul 2011 07:17:18 -0700 (PDT) From: Austin B. Yongye ybau...@yahoo.com Subject: Re: [gmx-users] Conversion of the GLYCAM dihedral parameters in the GROMACS format. To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 1311171438.14853.yahoomailclas...@web161422.mail.bf1.yahoo.com Content-Type: text/plain; charset=utf-8 So my questions are: how to convert it in the gromacs format ? I haven't done AMBER to GROMACS conversions. But a google search led me to this page. It's just a matter of knowing the different formats. http://ffamber.cnsm.csulb.edu Is it correct to use the absolute value of the multiplicity in my parameters and use the negative values of barrier heights when they are exist in the AMBER parameters? Since, I have noticed that in the AMBER ff port in GROMACS, the multiplicity values are always set to 0 and the barrier heights have sometime a negative value. So my questions are: how to convert it in the gromacs format ? Is it correct to use the absolute value of the multiplicity in my parameters and use the negative values of barrier heights when they are exist in the AMBER parameters? Since, I have noticed that in the AMBER ff port in GROMACS, the multiplicity values are always set to 0 and the barrier heights have sometime a negative value. Thank you again for your advice. SA- Message: 1 Date: Tue, 19 Jul 2011 11:08:55 -0700 (PDT) From: Austin B. Yongye ybau...@yahoo.com Subject: Re: [gmx-users] Conversion of the GLYCAM dihedral parameters in the GROMACS format. To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 1311098935.93905.yahoomailclas...@web161426.mail.bf1.yahoo.com Content-Type: text/plain; charset=utf-8 It is normal to have combinations of negative and positive values for the barrier heights. Those are just the best coefficients to reproduce some QM rotational energy curve during the parameterization. The negative periodicities are a convention from AMBER. They simply indicate that the dihedral angle potential has more than one term. For your example below: O2-P -OS-CP 10.10 0.0-3. Dimethyl phosphate 1 -0.50 0.0-2. 10.10 0.0 1 -3, -2 and 1 signify V3, V2 and V1 terms, respectively. Once a positive value is reached, terms for the O2-P-OS-CP potential have been completely accounted for. Hope that helps. Austin- --- On Tue, 7/19/11, Mark Abraham mark.abra...@anu.edu.au wrote: From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] Conversion of the GLYCAM dihedral parameters in the GROMACS format. To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Tuesday, July 19, 2011, 7:08 AM On 19/07/2011 11:56 PM, sa wrote: Dear GROMCS users, I am trying to convert some GLYCAM parameters in GROMACS format. For this purpose, I am using the latest GLYCAM parameters downloaded from the RJ. Woods’ website and the examples given in the acpype code (here for the dihedral angles) : http://code.google.com/p/acpype/source/browse/trunk/acpypi.py?spec=svn9r=9redir=1 --- # dihedralidivfbarrier hight/2 kcal/mol phase degrees periodicity comments X -ca-ca-X4 14.500* 180.000 2.000 intrpol.bsd.on C6H6 * to convert to gmx: 14.5/4 * 4.184 * 2 (?) (yes in amb2gmx, no in topolbuild, why?) = 30.334 or 15.167 kJ/mol # X -CA-CA-X4 14.50180.0 2. intrpol.bsd.on C6H6 (from parm99.dat) # X-CA-CA-X 330.33400 0.0 -30.33400 0.0 0.0 0.0 ; intrpol.bsd.on C6H6 --- I have no problems with the parameters for proteins. But, in case of the GLYCAM parameters, I am a little confused about the conversion of dihedral force constants (DFC), especially when the DFC and the periodicity values are 0 for example for this torsion: O2-P -OS-CP 10.10 0.0-3. Dimethyl phosphate 1 -0.50 0.0-2. 10.10 0.0 1 Where only a positive value makes sense, sometimes people use negative values to indicate some special functional form. This can be easier to code. Regardless, you'll have to check out the GLYCAM documentation and see what is meant, before you
[gmx-users] Conversion of the GLYCAM dihedral parameters in the GROMACS format.
Thank you Austin, for the clarification, So my questions are: how to convert it in the gromacs format ? Is it correct to use the absolute value of the multiplicity in my parameters and use the negative values of barrier heights when they are exist in the AMBER parameters? Since, I have noticed that in the AMBER ff port in GROMACS, the multiplicity values are always set to 0 and the barrier heights have sometime a negative value. Thank you again for your advice. SA- Message: 1 Date: Tue, 19 Jul 2011 11:08:55 -0700 (PDT) From: Austin B. Yongye ybau...@yahoo.com Subject: Re: [gmx-users] Conversion of the GLYCAM dihedral parameters in the GROMACS format. To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 1311098935.93905.yahoomailclas...@web161426.mail.bf1.yahoo.com Content-Type: text/plain; charset=utf-8 It is normal to have combinations of negative and positive values for the barrier heights. Those are just the best coefficients to reproduce some QM rotational energy curve during the parameterization. The negative periodicities are a convention from AMBER. They simply indicate that the dihedral angle potential has more than one term. For your example below: O2-P -OS-CP 10.10 0.0-3. Dimethyl phosphate 1 -0.50 0.0-2. 10.10 0.0 1 -3, -2 and 1 signify V3, V2 and V1 terms, respectively. Once a positive value is reached, terms for the O2-P-OS-CP potential have been completely accounted for. Hope that helps. Austin- --- On Tue, 7/19/11, Mark Abraham mark.abra...@anu.edu.au wrote: From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] Conversion of the GLYCAM dihedral parameters in the GROMACS format. To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Tuesday, July 19, 2011, 7:08 AM On 19/07/2011 11:56 PM, sa wrote: Dear GROMCS users, I am trying to convert some GLYCAM parameters in GROMACS format. For this purpose, I am using the latest GLYCAM parameters downloaded from the RJ. Woods’ website and the examples given in the acpype code (here for the dihedral angles) : http://code.google.com/p/acpype/source/browse/trunk/acpypi.py?spec=svn9r=9redir=1 --- # dihedralidivfbarrier hight/2 kcal/mol phase degrees periodicity comments X -ca-ca-X4 14.500* 180.000 2.000 intrpol.bsd.on C6H6 * to convert to gmx: 14.5/4 * 4.184 * 2 (?) (yes in amb2gmx, no in topolbuild, why?) = 30.334 or 15.167 kJ/mol # X -CA-CA-X4 14.50180.0 2. intrpol.bsd.on C6H6 (from parm99.dat) # X-CA-CA-X 330.33400 0.0 -30.33400 0.0 0.0 0.0 ; intrpol.bsd.on C6H6 --- I have no problems with the parameters for proteins. But, in case of the GLYCAM parameters, I am a little confused about the conversion of dihedral force constants (DFC), especially when the DFC and the periodicity values are 0 for example for this torsion: O2-P -OS-CP 10.10 0.0-3. Dimethyl phosphate 1 -0.50 0.0-2. 10.10 0.0 1 Where only a positive value makes sense, sometimes people use negative values to indicate some special functional form. This can be easier to code. Regardless, you'll have to check out the GLYCAM documentation and see what is meant, before you can address how to convert it into a GROMACS format. Obviously the contents of parts of chapter 4 and 5 of the manual will be important. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Conversion of the GLYCAM dihedral parameters in the GROMACS format.
Dear GROMCS users, I am trying to convert some GLYCAM parameters in GROMACS format. For this purpose, I am using the latest GLYCAM parameters downloaded from the RJ. Woods’ website and the examples given in the acpype code (here for the dihedral angles) : http://code.google.com/p/acpype/source/browse/trunk/acpypi.py?spec=svn9r=9redir=1 --- # dihedralidivfbarrier hight/2 kcal/mol phase degrees periodicity comments X -ca-ca-X4 14.500* 180.000 2.000 intrpol.bsd.on C6H6 * to convert to gmx: 14.5/4 * 4.184 * 2 (?) (yes in amb2gmx, no in topolbuild, why?) = 30.334 or 15.167 kJ/mol # X -CA-CA-X4 14.50180.0 2. intrpol.bsd.on C6H6 (from parm99.dat) # X-CA-CA-X 330.33400 0.0 -30.33400 0.0 0.0 0.0 ; intrpol.bsd.on C6H6 --- I have no problems with the parameters for proteins. But, in case of the GLYCAM parameters, I am a little confused about the conversion of dihedral force constants (DFC), especially when the DFC and the periodicity values are 0 for example for this torsion: O2-P -OS-CP 10.10 0.0-3. Dimethyl phosphate 1 -0.50 0.0-2. 10.10 0.0 1 Thank you in advance, for your help SA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: About the %SS values in the output of do_dssp
Ok Thank you Justin for this clarification
sa wrote:
Dear All,
I have simulated 6 peptides (with 7 AA each capped in N and C termini)
in water and trehalose. During all the simulation time, the six peptides
have b-sheet conformations. I would like to calculate the average % of
secondary structure for the 6 peptides over the course of run. So I have
read the subject reported in the following link
http://redmine.gromacs.org/issues/683 and used the following command for
the two first frames
/work/sa001/gmx-post4.5.3/bin/do_dssp_mpi -f *-Center_All.xtc -s
run_1.tpr -tu ps -dt 1 -b 1 -e 5 -o
6_Peptide_53A6_Trehal_Pref_SS.xpm -sss
6_Peptide_53A6_Trehal_Pref_HEBT.dat -ssdump
6_Peptide_53A6_Trehal_Dump_SS.dat -sc test.xvg
I obtained the following output for my six peptides
@TYPE xy
@ subtitle Structure = + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + B-Sheet + + + + + +
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend Structure
@ s1 legend Coil
@ s2 legend B-Sheet
@ s3 legend Chain_Separator
2301230 5
4301230 5
# Totals60246010
# SS %0.64 0.26 0.64 0.11
I can understand how the %SS values are obtained in the example given in
http://redmine.gromacs.org/issues/683, but not in my case. Could you
tell me how the %SS is obtained the output above.
Like any other average. From the code:
/* now print percentages */
fprintf(fp, %-8s %5.2f, # SS %, total_count / (real) (mat-nx *
mat-ny));
for(s=0; smat-nmap; s++)
{
fprintf(fp, %5.2f,total[s] / (real) (mat-nx * mat-ny));
}
fprintf(fp,\n);
So the total number of secondary structure elements is divided by the
product of
(number of frames * number of total residues).
Your results are affected by the problem I mentioned in the issue report
you
quote. You have 42 residues, but since chain separators count as residues,
the
calculations are all done out of 47 residues instead. You'll have to
either
modify the code to account for this problem or simply re-calculate the
averages
yourself.
-Justin
Thank you in advance for your help
SA
--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
--
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[gmx-users] About the %SS values in the output of do_dssp
Dear All, I have simulated 6 peptides (with 7 AA each capped in N and C termini) in water and trehalose. During all the simulation time, the six peptides have b-sheet conformations. I would like to calculate the average % of secondary structure for the 6 peptides over the course of run. So I have read the subject reported in the following link http://redmine.gromacs.org/issues/683and used the following command for the two first frames /work/sa001/gmx-post4.5.3/bin/do_dssp_mpi -f *-Center_All.xtc -s run_1.tpr -tu ps -dt 1 -b 1 -e 5 -o 6_Peptide_53A6_Trehal_Pref_SS.xpm -sss 6_Peptide_53A6_Trehal_Pref_HEBT.dat -ssdump 6_Peptide_53A6_Trehal_Dump_SS.dat -sc test.xvg I obtained the following output for my six peptides @TYPE xy @ subtitle Structure = + + + + + + + + + + + + + + + + + + + + + + + + + + + + B-Sheet + + + + + + @ view 0.15, 0.15, 0.75, 0.85 @ legend on @ legend box on @ legend loctype view @ legend 0.78, 0.8 @ legend length 2 @ s0 legend Structure @ s1 legend Coil @ s2 legend B-Sheet @ s3 legend Chain_Separator 2301230 5 4301230 5 # Totals60246010 # SS %0.64 0.26 0.64 0.11 I can understand how the %SS values are obtained in the example given in http://redmine.gromacs.org/issues/683, but not in my case. Could you tell me how the %SS is obtained the output above. Thank you in advance for your help SA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Different g_sas values between AMBER, CHARMM and GROMOS ff for DPC
Thank you David, My micelle simulated with the GROMOS ff slightly differs (size and shape) from the two others micelles, so i expected that the values total SAS value slightly differ. In case of the headgroup, they are located in the micelle interface region, so the SAS in case of the micelle simulated with GROMOS should be not so different (36 % less) than the others micelles You said that In order for g_sas to work with gromos force field one would have to increase the radius of the carbon atoms. For the 54 atoms the default value will be used. How to do that ? and for all the carbon atoms (including the headgroup carbon atoms). Thank you SA On 2011-04-09 19.06, sa wrote: Dear All, I have simulated three DPC micelles with the same size (54 lipids) with different force fields (CHARMM, AMBER et GROMOS53A6) and computed the average accessible surface areas for each lipids with g_sas (gmx4.5.3) I obtain the three average values for total DPC, the headgroup (phosphocholine) and the alkyl tail. Total (A2)Head Tail GROMOS53A6158.4 ± 4.8 54.8 ± 3.4 103.2 ± 3.8 AMBER 248.2 ± 8.7 76.2 ± 5.1 172.5 ± 5.2 CHARMM 242.7 ± 7.7 70.4 ± 4.1 172.4 ± 4.8 As you can see the ASA values are close between the micelles simulated with the CHARMM and AMBER ff, but larger than the values obtained from the micelle simulated with GROMOS ff especially for the headgroup. I am aware that CHARMM and AMBER are explicits ff whereas GROMOS is an united ff It is the reason I obtain a smaller values for GROMOS compared to two others ones ? Does g_sas tool take into account this. I have also noted when I use g_sas i obtain the following message WARNING: masses and atomic (Van der Waals) radii will be determined based on residue and atom names. These numbers can deviate from the correct mass and radius of the atom type. WARNING: could not find a Van der Waals radius for 54 atoms It is important ? Given your observations above, don't you think it might be? In order for g_sas to work with gromos force field one would have to increase the radius of the carbon atoms. For the 54 atoms the default value will be used. Thank you in advance for your advices. SA -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Different g_sas values between AMBER, CHARMM and GROMOS ff for DPC
Thank you David A bientôt SA -- Message: 1 Date: Sun, 10 Apr 2011 11:17:15 +0200 From: David van der Spoel sp...@xray.bmc.uu.se Subject: Re: [gmx-users] Different g_sas values between AMBER, CHARMM and GROMOS ff for DPC To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4da1759b.2000...@xray.bmc.uu.se Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 2011-04-10 11.11, sa wrote: Thank you David, My micelle simulated with the GROMOS ff slightly differs (size and shape) from the two others micelles, so i expected that the values total SAS value slightly differ. In case of the headgroup, they are located in the micelle interface region, so the SAS in case of the micelle simulated with GROMOS should be not so different (36 % less) than the others micelles You said that In order for g_sas to work with gromos force field one would have to increase the radius of the carbon atoms. For the 54 atoms the default value will be used. How to do that ? and for all the carbon atoms (including the headgroup carbon atoms). edit vdwradii.dat. Then be careful to use an atom name that is specific for the FF such that your Amber and Charmm runs keep the correct value. Thank you SA On 2011-04-09 19.06, sa wrote: Dear All, I have simulated three DPC micelles with the same size (54 lipids) with different force fields (CHARMM, AMBER et GROMOS53A6) and computed the average accessible surface areas for each lipids with g_sas (gmx4.5.3) I obtain the three average values for total DPC, the headgroup (phosphocholine) and the alkyl tail. Total (A2)Head Tail GROMOS53A6158.4 ± 4.8 54.8 ± 3.4 103.2 ± 3.8 AMBER 248.2 ± 8.7 76.2 ± 5.1 172.5 ± 5.2 CHARMM 242.7 ± 7.7 70.4 ± 4.1 172.4 ± 4.8 As you can see the ASA values are close between the micelles simulated with the CHARMM and AMBER ff, but larger than the values obtained from the micelle simulated with GROMOS ff especially for the headgroup. I am aware that CHARMM and AMBER are explicits ff whereas GROMOS is an united ff It is the reason I obtain a smaller values for GROMOS compared to two others ones ? Does g_sas tool take into account this. I have also noted when I use g_sas i obtain the following message WARNING: masses and atomic (Van der Waals) radii will be determined based on residue and atom names. These numbers can deviate from the correct mass and radius of the atom type. WARNING: could not find a Van der Waals radius for 54 atoms It is important ? Given your observations above, don't you think it might be? In order for g_sas to work with gromos force field one would have to increase the radius of the carbon atoms. For the 54 atoms the default value will be used. Thank you in advance for your advices. SA -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se http://folding.bmc.uu.se -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! End of gmx-users Digest, Vol 84, Issue 80 * -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Different g_sas values between AMBER, CHARMM and GROMOS ff for DPC
Dear All, I have simulated three DPC micelles with the same size (54 lipids) with different force fields (CHARMM, AMBER et GROMOS53A6) and computed the average accessible surface areas for each lipids with g_sas (gmx4.5.3) I obtain the three average values for total DPC, the headgroup (phosphocholine) and the alkyl tail. Total (A2)Head Tail GROMOS53A6158.4 ± 4.8 54.8 ± 3.4 103.2 ± 3.8 AMBER 248.2 ± 8.7 76.2 ± 5.1 172.5 ± 5.2 CHARMM 242.7 ± 7.7 70.4 ± 4.1 172.4 ± 4.8 As you can see the ASA values are close between the micelles simulated with the CHARMM and AMBER ff, but larger than the values obtained from the micelle simulated with GROMOS ff especially for the headgroup. I am aware that CHARMM and AMBER are explicits ff whereas GROMOS is an united ff It is the reason I obtain a smaller values for GROMOS compared to two others ones ? Does g_sas tool take into account this. I have also noted when I use g_sas i obtain the following message WARNING: masses and atomic (Van der Waals) radii will be determined based on residue and atom names. These numbers can deviate from the correct mass and radius of the atom type. WARNING: could not find a Van der Waals radius for 54 atoms It is important ? Thank you in advance for your advices. SA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] RE: mathematical expression to obtain the C6 and C12 LJ terms for the GROMOSXX ff family
Dear All, Finally, I resolved my problem by contacting the author of the paper (thanks to D. Poger). They gave me the correct value for the epsilon and sigma (0.2137 nm instead of 0.3137 nm in the paper). SA Message: 2 Date: Tue, 29 Mar 2011 09:45:34 +1100 From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] Re: mathematical expression to obtain the C6 and C12 LJ terms for the GROMOSXX ff family To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4d910f8e.8050...@anu.edu.au Content-Type: text/plain; charset=iso-8859-1 On 29/03/2011 12:17 AM, sa wrote: OK, Pr van der Spoel, So what is the correct way to obtain LJ C6 and C12 values given in the [ atomtypes ] and in the [ nonbond_types] sections of ffnonbonded.itp if I have only the sigma and epsilon values. If understand well [ atomtypes ] section give the comb-rules for the atom with itself, correct ? And the nonbond_types section, the comb-rules with the other atoms types. So if I take into account only the OM atom, as an example, why I obtained different values for C6 and C12 terms in the [ atomtypes ] section. Thank you again for your help. Section 5.3.3 of the manual goes through this. Mark -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20110329/ec6eec7f/attachment-0001.html -- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] mathematical expression to obtain the C6 and C12 LJ terms for the GROMOSXX ff family
Thank you Justin for your response I have tried g_sigeps with the OM type LJ values (sigma (nm) = 0.3137 and epsilon (kj/mol) = 1.2231 given in Poger et al. Paper (JCC Vol 31, 6, 1117) as an example. Unfortunately i can't retrieve the C6 and C12 values given for the same in the GROMOS53A6 ffnonbonded.itp. I used the following command g_sigeps_mpi -sig 0.3137 -eps 1.2231 and obtained the output c6= 4.66239e-03, c12= 4.44320e-06 sigma = 0.31370, epsilon = 1.22310 Van der Waals minimum at 0.352116, V = -1.2231 Fit of Lennard Jones (12-6) to Buckingham: A = 199065, B = 34.0796, C = 0.00466239 Back Off! I just backed up potje.xvg to ./#potje.xvg.8# gcq#342: Ich war schwanger, mir gings zum kotzen (Nina Hagen) Did I miss something ? Thank you again for your help SA sa wrote: Dear All, I would like to compute the C6 and C12 LJ terms for the GROMOS 53A6 ff for a new atom type and incorporate them in my ffnonbonded.itp. Does anybody know the mathematical expressions used to obtain these terms from a sigma (nm) and an epsilon (kj/mol) values manually. g_sigeps can do this for you. Otherwise, you can convert between the two common forms of the Lennard-Jones equation. -Justin Thank you for your help. SA -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: mathematical expression to obtain the C6 and C12 LJ terms for the GROMOSXX ff family
Sorry I forget to say in my previous mail that the values obtained by g_sigeps_mpi are not similar to the values given in the GROMOS53A6 ffnonbonded.itp for the OM atom. OM8 0.000 0.000 A 0.0022619536 7.4149321e-07 So your advices are welcome. SA 2011/3/28 sa sagmx.m...@gmail.com Thank you Justin for your response I have tried g_sigeps with the OM type LJ values (sigma (nm) = 0.3137 and epsilon (kj/mol) = 1.2231 given in Poger et al. Paper (JCC Vol 31, 6, 1117) as an example. Unfortunately i can't retrieve the C6 and C12 values given for the same in the GROMOS53A6 ffnonbonded.itp. I used the following command g_sigeps_mpi -sig 0.3137 -eps 1.2231 and obtained the output c6= 4.66239e-03, c12= 4.44320e-06 sigma = 0.31370, epsilon = 1.22310 Van der Waals minimum at 0.352116, V = -1.2231 Fit of Lennard Jones (12-6) to Buckingham: A = 199065, B = 34.0796, C = 0.00466239 Back Off! I just backed up potje.xvg to ./#potje.xvg.8# gcq#342: Ich war schwanger, mir gings zum kotzen (Nina Hagen) Did I miss something ? Thank you again for your help SA sa wrote: Dear All, I would like to compute the C6 and C12 LJ terms for the GROMOS 53A6 ff for a new atom type and incorporate them in my ffnonbonded.itp. Does anybody know the mathematical expressions used to obtain these terms from a sigma (nm) and an epsilon (kj/mol) values manually. g_sigeps can do this for you. Otherwise, you can convert between the two common forms of the Lennard-Jones equation. -Justin Thank you for your help. SA -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: gmx-users Digest, Vol 83, Issue 196
Thank you Justin, It is good to know i am not alone to not understand. So I will ask to the authors the reason of this discrepancy. Bye SA 2011/3/28 gmx-users-requ...@gromacs.org - next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20110328/33c5a2e5/attachment-0001.html -- Message: 3 Date: Mon, 28 Mar 2011 07:27:11 -0400 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] mathematical expression to obtain the C6 and C12 LJ terms for the GROMOSXX ff family To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4d90708f.7000...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed sa wrote: Thank you Justin for your response I have tried g_sigeps with the OM type LJ values (sigma (nm) = 0.3137 and epsilon (kj/mol) = 1.2231 given in Poger et al. Paper (JCC Vol 31, 6, 1117) as an example. Unfortunately i can't retrieve the C6 and C12 values given for the same in the GROMOS53A6 ffnonbonded.itp. I used the following command I cannot explain this discrepancy. Going back to the actual 53A6 source (Oostenbrink et al. JCC 2004: 25: 1656-1676), the parameters in ffnonbonded.itp are correct with respect to the original force field. The fact that Poger et al. claim the parameters are the same does not make sense to me. You may wish to contact the authors of that paper directly if you have questions about reproducing their results. I also find it curious that they list their values in sigma/epsilon rather than the conventional C6/C12 used by Gromos96 force fields. -Justin g_sigeps_mpi -sig 0.3137 -eps 1.2231 and obtained the output c6= 4.66239e-03, c12= 4.44320e-06 sigma = 0.31370, epsilon = 1.22310 Van der Waals minimum at 0.352116, V = -1.2231 Fit of Lennard Jones (12-6) to Buckingham: A = 199065, B = 34.0796, C = 0.00466239 Back Off! I just backed up potje.xvg to ./#potje.xvg.8# gcq#342: Ich war schwanger, mir gings zum kotzen (Nina Hagen) Did I miss something ? Thank you again for your help SA sa wrote: Dear All, I would like to compute the C6 and C12 LJ terms for the GROMOS 53A6 ff for a new atom type and incorporate them in my ffnonbonded.itp. Does anybody know the mathematical expressions used to obtain these terms from a sigma (nm) and an epsilon (kj/mol) values manually. g_sigeps can do this for you. Otherwise, you can convert between the two common forms of the Lennard-Jones equation. -Justin Thank you for your help. SA -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- Message: 4 Date: Mon, 28 Mar 2011 14:07:31 +0200 From: sa sagmx.m...@gmail.com Subject: [gmx-users] Re: mathematical expression to obtain the C6 and C12 LJ terms for the GROMOSXX ff family To: gmx-users@gromacs.org Message-ID: AANLkTimWtTB4V_=ngpbvp9ga4zrnaroxnh-rqt-pr...@mail.gmail.com Content-Type: text/plain; charset=iso-8859-1 Sorry I forget to say in my previous mail that the values obtained by g_sigeps_mpi are not similar to the values given in the GROMOS53A6 ffnonbonded.itp for the OM atom. OM8 0.000 0.000 A 0.0022619536 7.4149321e-07 So your advices are welcome. SA 2011/3/28 sa sagmx.m...@gmail.com Thank you Justin for your response I have tried g_sigeps with the OM type LJ values (sigma (nm) = 0.3137 and epsilon (kj/mol) = 1.2231 given in Poger et al. Paper (JCC Vol 31, 6, 1117) as an example. Unfortunately i can't retrieve the C6 and C12 values given for the same in the GROMOS53A6 ffnonbonded.itp. I used the following command g_sigeps_mpi -sig 0.3137 -eps 1.2231 and obtained the output c6= 4.66239e-03, c12= 4.44320e-06 sigma = 0.31370, epsilon = 1.22310 Van der Waals minimum at 0.352116, V = -1.2231 Fit of Lennard Jones (12-6) to Buckingham: A = 199065, B = 34.0796, C = 0.00466239 Back Off! I just backed up potje.xvg to ./#potje.xvg.8# gcq#342: Ich war schwanger, mir gings zum kotzen
Re: [gmx-users] Re: mathematical expression to obtain the C6 and C12 LJ terms for the GROMOSXX ff family
OK, Pr van der Spoel, So what is the correct way to obtain LJ C6 and C12 values given in the [ atomtypes ] and in the [ nonbond_types] sections of ffnonbonded.itp if I have only the sigma and epsilon values. If understand well [ atomtypes ] section give the comb-rules for the atom with itself, correct ? And the nonbond_types section, the comb-rules with the other atoms types. So if I take into account only the OM atom, as an example, why I obtained different values for C6 and C12 terms in the [ atomtypes ] section. Thank you again for your help. SA -- Message: 2 Date: Mon, 28 Mar 2011 14:13:44 +0200 From: David van der Spoel sp...@xray.bmc.uu.se Subject: Re: [gmx-users] Re: mathematical expression to obtain the C6 and C12 LJ terms for the GROMOSXX ff family To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4d907b78.20...@xray.bmc.uu.se Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 2011-03-28 14.07, sa wrote: Sorry I forget to say in my previous mail that the values obtained by g_sigeps_mpi are not similar to the values given in the GROMOS53A6 ffnonbonded.itp for the OM atom. OM8 0.000 0.000 A 0.0022619536 7.4149321e-07 Difficult to compare this way. note that gromos does not use simple combination rules. For OM there are different C12 (IIRC) depending on the interacting atom. You should look only at the [ nonbond_types] section So your advices are welcome. SA 2011/3/28 sa sagmx.m...@gmail.com mailto:sagmx.m...@gmail.com Thank you Justin for your response I have tried g_sigeps with the OM type LJ values (sigma (nm) = 0.3137 and epsilon (kj/mol) = 1.2231 given in Poger et al. Paper (JCC Vol 31, 6, 1117) as an example. Unfortunately i can't retrieve the C6 and C12 values given for the same in the GROMOS53A6 ffnonbonded.itp. I used the following command g_sigeps_mpi -sig 0.3137 -eps 1.2231 and obtained the output c6= 4.66239e-03, c12= 4.44320e-06 sigma = 0.31370, epsilon = 1.22310 Van der Waals minimum at 0.352116, V = -1.2231 Fit of Lennard Jones (12-6) to Buckingham: A = 199065, B = 34.0796, C = 0.00466239 Back Off! I just backed up potje.xvg to ./#potje.xvg.8# gcq#342: Ich war schwanger, mir gings zum kotzen (Nina Hagen) Did I miss something ? Thank you again for your help SA sa wrote: Dear All, I would like to compute the C6 and C12 LJ terms for the GROMOS 53A6 ff for a new atom type and incorporate them in my ffnonbonded.itp. Does anybody know the mathematical expressions used to obtain these terms from a sigma (nm) and an epsilon (kj/mol) values manually. g_sigeps can do this for you. Otherwise, you can convert between the two common forms of the Lennard-Jones equation. -Justin Thank you for your help. SA -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] mathematical expression to obtain the C6 and C12 LJ terms for the GROMOSXX ff family
Dear All, I would like to compute the C6 and C12 LJ terms for the GROMOS 53A6 ff for a new atom type and incorporate them in my ffnonbonded.itp. Does anybody know the mathematical expressions used to obtain these terms from a sigma (nm) and an epsilon (kj/mol) values manually. Thank you for your help. SA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: gmx-users Digest, Vol 83, Issue 106
Thank you Angel, I will try your suggestion. Cheers SA Hi very recently I faced the same problem with a system that gives micelles of different geometries and, as far as I saw, g_order don't do that. Then I decided to compute a kind of local order parameters defined as: S_i=(3 cos(\theta)-1)/2 where theta is the angle between the segments joining the carbon atoms (i-1,i+1) and (i, i+2) in a linear C-chain. Perhaps you find this reasonable for your analysis... Cheers, Ángel. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_order for DPC alkyl chain in the micelle
Hi all This message is related with my previous message (see below) about the calculation of the order value for the DPC alkyl chain in a micelle. So if I understand well the previous angel's message, I need to compute the theta angle between the 2 vectors defined by the (i-1,i+1) and (i, i+2). So for carbon atom C14, I have created an index file with two groups defined as following aC14 | aC16 and aC14 | aC16 with make_ndx_mpi and used the command g_sgangle_mpi -s run_1.tpr -f *.xtc -b 10 -e 101000 -n index.ndx and choose the C13_C15 and C14_C16 groups. Unfortunately i obtain the following error Group C13_C15 contains the following atoms: Atomname 0: C13 Atomname 1: C15 Atomname 2: C13 Atomname 3: C15 Atomname 4: C13 Atomname 5: C15 Atomname 6: C13 Atomname 7: C15 Atomname 8: C13 Atomname 9: C1 ... Group C14_C16 contains the following atoms: Atomname 0: C14 Atomname 1: C16 Atomname 2: C14 Atomname 3: C16 Atomname 4: C14 ... Atomname 105: C16 Atomname 106: C14 Atomname 107: C16 Careful: distance only makes sense in some situations. Reading frame 0 time 10.000 Back Off! I just backed up sg_angle.xvg to ./#sg_angle.xvg.2# --- Program g_sgangle_mpi, VERSION 4.5.3 Source code file: gmx_sgangle.c, line: 127 Fatal error: Something wrong with contents of index file. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Did I make a error, what is the correct approach. to obtain the angle between 2 vectors ? Thank you in advance SA -- Message: 3 Date: Wed, 16 Mar 2011 10:06:44 +0100 From: ?ngel Pi?eiro angel.pine...@usc.es Subject: Re: [gmx-users] Re: gmx-users Digest, Vol 83, Issue 106 To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 1300266404.6843.29.camel@arginine Content-Type: text/plain; charset=utf-8 Then, please, let us know how it works for your systems. The results for my systems were exactly as expected. This allows to evaluate the order of the C-chains regardless their orientation... but I do not know if there is a better method to do this. I would be happy to know the opinion of anyone else who want to try this or to propose an alternative method. Cheers, Ã ngel. On Wed, 2011-03-16 at 09:42 +0100, sa wrote: Thank you Angel, I will try your suggestion. Cheers SA Hi very recently I faced the same problem with a system that gives micelles of different geometries and, as far as I saw, g_order don't do that. Then I decided to compute a kind of local order parameters defined as: S_i=(3 cos(\theta)-1)/2 where theta is the angle between the segments joining the carbon atoms (i-1,i+1) and (i, i+2) in a linear C-chain. Perhaps you find this reasonable for your analysis... Cheers, Ã ngel. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: g_order for DPC alkyl chain in the micelle
Ok Justin, So which gmx tool i can use to obtain the angle between two vectors defined by two atom pairs ? SA sa wrote: Hi all This message is related with my previous message (see below) about the calculation of the order value for the DPC alkyl chain in a micelle. So if I understand well the previous angel's message, I need to compute the theta angle between the 2 vectors defined by the (i-1,i+1) and (i, i+2). So for carbon atom C14, I have created an index file with two groups defined as following aC14 | aC16 and aC14 | aC16 with make_ndx_mpi and used the command g_sgangle_mpi -s run_1.tpr -f *.xtc -b 10 -e 101000 -n index.ndx and choose the C13_C15 and C14_C16 groups. Unfortunately i obtain the following error Group C13_C15 contains the following atoms: Atomname 0: C13 Atomname 1: C15 Atomname 2: C13 Atomname 3: C15 Atomname 4: C13 Atomname 5: C15 Atomname 6: C13 Atomname 7: C15 Atomname 8: C13 Atomname 9: C1 ... Group C14_C16 contains the following atoms: Atomname 0: C14 Atomname 1: C16 Atomname 2: C14 Atomname 3: C16 Atomname 4: C14 ... Atomname 105: C16 Atomname 106: C14 Atomname 107: C16 Careful: distance only makes sense in some situations. Reading frame 0 time 10.000 Back Off! I just backed up sg_angle.xvg to ./#sg_angle.xvg.2# --- Program g_sgangle_mpi, VERSION 4.5.3 Source code file: gmx_sgangle.c, line: 127 Fatal error: Something wrong with contents of index file. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Did I make a error, what is the correct approach. to obtain the angle between 2 vectors ? Per the description in g_sgangle -h, groups can only be two or three atoms in size. It seems as if this tool would be very inefficient for any more than a few calculations. -Justin Thank you in advance SA -- Message: 3 Date: Wed, 16 Mar 2011 10:06:44 +0100 From: ?ngel Pi?eiro angel.pine...@usc.es mailto: angel.pine...@usc.es Subject: Re: [gmx-users] Re: gmx-users Digest, Vol 83, Issue 106 To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org Message-ID: 1300266404.6843.29.camel@arginine Content-Type: text/plain; charset=utf-8 Then, please, let us know how it works for your systems. The results for my systems were exactly as expected. This allows to evaluate the order of the C-chains regardless their orientation... but I do not know if there is a better method to do this. I would be happy to know the opinion of anyone else who want to try this or to propose an alternative method. Cheers, Ã ngel. On Wed, 2011-03-16 at 09:42 +0100, sa wrote: Thank you Angel, I will try your suggestion. Cheers SA Hi very recently I faced the same problem with a system that gives micelles of different geometries and, as far as I saw, g_order don't do that. Then I decided to compute a kind of local order parameters defined as: S_i=(3 cos(\theta)-1)/2 where theta is the angle between the segments joining the carbon atoms (i-1,i+1) and (i, i+2) in a linear C-chain. Perhaps you find this reasonable for your analysis... Cheers, Ã ngel. -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_order for DPC alkyl chain in the micelle
OK Angel, I will contact you off-list SA Dear SA To be honest I am not sure this can be done by using g_angle, I used my own code for this calculation. I could send it to you if you send me a message off the list... but I would prefer to talk with a non-anonymous. Cheers, Ã ngel. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_order for DPC alkyl chain in the micelle
Dear all, I would like to compute the order parameter tensor elements of a DPC micelle with respect to a vector direction (for example the vector from the center of mass of the micelle to the phosphorus atom). It is possible with g_order (4.5.3). if yes how ? Thank you in advance. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Dihedral angles distribution
Dear GMXusers I would like to obtain the normalized dihedral distribution of the alkyl chain of DPC molecules simulated with the CHARMM ff and GMX4.5.3. So i used the g_angle tool. I have constructed an index file which contain the 9 corresponding angles with make_index_mpi: a C12 | a C13 | a C14 | a C15 --- consecutive atoms ... a C20 | a C21 | a C22 | aC23 and used g_angle command g_angle_mpi -f *.xtc -ov DPC-Self-CHA_100-155ns-Angle_0_Dihed.xvg -b 10 -e 11 -n Tail_dihedral_index.ndx -type dihedral For example by choosing the C15_C16_C17_C18 dihedral angle located in the middle of the alkyl chain, i obtain an average value 0° (!!) and the following figure http://www.hostingpics.net/viewer.php?id=825755angdist.png This is not what i expect How to obtain simply the classical normalized function from g_angle ? Thank you in advance for your advices SA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: gmx-users Digest, Vol 83, Issue 40
Yes justin, the average is not 0 but around 0° (0.584577). But how to obtain the Average normalized dihedral distribution for example this dihedral? is few words the figure with g_angle ? http://cmt.dur.ac.uk/sjc/thesis_dlc/node106.html Thank you again sa wrote: Dear GMXusers I would like to obtain the normalized dihedral distribution of the alkyl chain of DPC molecules simulated with the CHARMM ff and GMX4.5.3. So i used the g_angle tool. I have constructed an index file which contain the 9 corresponding angles with make_index_mpi: a C12 | a C13 | a C14 | a C15 --- consecutive atoms ... a C20 | a C21 | a C22 | aC23 and used g_angle command g_angle_mpi -f *.xtc -ov DPC-Self-CHA_100-155ns-Angle_0_Dihed.xvg -b 10 -e 11 -n Tail_dihedral_index.ndx -type dihedral For example by choosing the C15_C16_C17_C18 dihedral angle located in the middle of the alkyl chain, i obtain an average value 0° (!!) and the following figure http://www.hostingpics.net/viewer.php?id=825755angdist.png This is not what i expect How to obtain simply the classical normalized function from g_angle ? You're taking an average of the histogram of the angles, which I don't think actually corresponds to the true average. Your biggest peaks are at +/- 180 (i.e., trans dihedral), so I suspect your mean is likely not really 0. Use g_angle -ov to get an actual average over time. -Justin Thank you in advance for your advices SA -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: gmx-users Digest, Vol 83, Issue 41
OK, i will try your suggestion.
Thank you
SA
sa wrote:
Yes justin, the average is not 0 but around 0° (0.584577). But how to
obtain the Average normalized dihedral distribution for example
this dihedral? is few words the figure with g_angle ?
http://cmt.dur.ac.uk/sjc/thesis_dlc/node106.html
The output you will get from Gromacs will have all angles within the range
of
{-180..180}, not {0..360}, as shown in that plot. I think this simply
derives
from a difference in convention. You would have to post-process the data
to
shift the angles to correspond to the display range you want. Gromacs does
not
do this for you. To get the correct average angle, use g_angle
-noperiodic.
-Justin
Thank you again
sa wrote:
Dear GMXusers
I would like to obtain the normalized dihedral distribution
of the
alkyl chain of DPC molecules simulated with the CHARMM ff and
GMX4.5.3.
So i used the g_angle tool. I have constructed an index file which
contain the 9 corresponding angles with make_index_mpi:
a C12 | a C13 | a C14 | a C15 --- consecutive atoms
...
a C20 | a C21 | a C22 | aC23
and used g_angle command
g_angle_mpi -f *.xtc -ov DPC-Self-CHA_100-155ns-Angle_0_Dihed.xvg
-b
10 -e 11 -n Tail_dihedral_index.ndx -type dihedral
For example by choosing the C15_C16_C17_C18 dihedral angle located
in
the middle of the alkyl chain, i obtain an average value 0° (!!)
and the
following figure
http://www.hostingpics.net/viewer.php?id=825755angdist.png
This is not what i expect How to obtain simply the classical
normalized
function from g_angle ?
You're taking an average of the histogram of the angles, which I
don't think
actually corresponds to the true average. Your biggest peaks are at
+/- 180
(i.e., trans dihedral), so I suspect your mean is likely not really
0. Use
g_angle -ov to get an actual average over time.
-Justin
Thank you in advance for your advices
SA
--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu http://vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
--
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
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http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] How to obtain the average radial density functions relative to the center of mass with g_rdf.
Dear GMXusers, Last week, i asked a question about the calculation of average radial density functions relative to the center of mass of a micelle formed with DPC molecules (rdf). Unfortunately i received no response. So i re ask my question. So I would like to obtain the average rdf function (in g/cm3) for different groups of my micellar system (such as the headgroup, alkyl tail of the surfactant and water). For this purpose, I have created a index file where all DPC atoms (heavy and H atoms ) are separated in different groups and use the following command with g_rdf (4.5.3) g_rdf_mpi -f *_Center_All.xtc -s run_1.tpr -o DPC-Self-AMB_100-155ns_DPC_RDF.xvg -b 10 -e 155000 -norm -com -n index_Radial_Profile_DPC.ndx I chose DPC atoms as a reference group and obtain the rdf curves for the DPC headgroup, alkyl tail and water. I obtain the following figure : http://img4.hostingpics.net/pics/213680DPCSelfAMB100155nsRDF.jpg I don't understand why the curves amplitudes for the headgroup, alkyl tail are so high (and what is the unity ?), For example for the C12 alkyl chain rdf I understand well the help of the g_rdf tool, I expect a rdf with a density maxima around 0.8 - 0.9 g/cm3. Did i compute the expected function with above command ? If not, how to obtain the rdf (in g/cm3) for each components ? Thanks for the help. SA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Values of radial density profiles
Dear All I would like to compute the radial density function rho(r) (in g/cm3) of different parts of micelle formed with DPC molecules (such as headgroup, alkyl tail and water) relative to the center of mass of the aggregate. I have constructed an index files containing all the atoms of the surfactant headgroup and alkyl chain and used g_rdf (4.5.3): /work/cont003/abel01/gmx4.5.3/bin/g_rdf_mpi -f *_Center_All.xtc -s run_1.tpr -o DPC-Self-AMB_100-155ns_HEADGROUP_RDF.xvg -b 10 -e 155000 -norm -com -n index_Radial_Profile_DPC.ndx For water, as expected, I obtained a RDF profile where rho (r) values tend to the water density (~1g/cm3) near the simulation edge box. For the headgroup and the alkyl tail of the DPC, it is not the case since I obtained two peaks with rho (r) values higher than the density a phosphocholine group and a dodecyl alkyl chain (in my case 26.4 and 16.4 ). What is wrong with command used above. Did i forget something ? Thank you in advance for your help. SA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] How to obtain the semi-axis lengths from inertia tensor for an aggregate
Dear all, I would to obtain the semi-axis lengths of a simulated micelle (in Ang) with gromacs. So I have used the g_principal tool (correct ?). My input command was g_principal_mpi -f bDM-Self_Only_DDM_Center.xtc -s bDM_only.tpr -a1 bDM_Self_Axe1 -a2 bDM_Self_Axe2 -a3 bDM_Self_Axe3 -om bDM_Self_MOI.xvg -dt 10 -b 5 -e 10 bDM_Mol.txt Four files *Self_Axe*.dat and bDM_Self_MOI.dat were generated as expected with four columns. How to deduce the semiaxis lenghts from these files *Self_Axe*.dat files. The documentation of this tool is not very clear. A similar question was posted in the mailing list few days ago, unfortunately no response was given: http://www.mail-archive.com/gmx-users@gromacs.org/msg35963.html Thanks in advance SA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Re: Discrepancy between -chargegrp and -nochargegrp in simulations with CHARMM ff, Why ?
Dear all, I come back to you with my problem between -chargegrp and -nochargegrp with new results which are contradict my previous findings. Indeed, in my previous message i have suggested that the discrepancies between -chargegrp and -nochargegrp in my simulations of a 25 AA peptide in TIP3P water. I suspect that this discrepancy came probably from an old version of the CHARMM27 ff and the used in my simulations. To test this hypothesis i have done six additional simulations of the same system (a 25 AA peptide in TIP3P water) with the new released of the CHARMM27 ff and gromacs versions 4.5.1 and 4.5.3 I have done three simulation of with a *.top file generated by pdb2gromacs v. 4.5.3 and modified by hand to change the charge groups distribution in the peptide atoms according to the original CHARMM force field and to mimic the -chargegrp option available in the previous version of gromacs. Three others MD were also done with *.top generated with pdb2gromacs of gromacs 4.5.3 (i.e. with one charge group per atom). 1- gromacs4.5.1 and CHARMM27.ff - gromacs 4.5.1* 2- gromacs4.5.3 and CHARMM27.ff - gromacs 4.5.3* 3- gromacs4.5.3 and CHARMM27.ff and MD parameters used by Bjelkmar et al. (J. Chem. Theory Comput. 2010, 6, 459–466- gromacs 4.5.3** non-bonded md parameters used in * simulations continuation= no; Restarting after NPT vdw-type= cut-off rvdw= 1.0 rlist = 0.9 coulombtype = PME rcoulomb = 0.9 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order= 4 ewald_rtol = 1e-05 optimize_fft= yes To summarize, as shown in the two figures accessible with the two links below (hosted by hostingpics.net), all the peptides remain in their helix conformation and no significant differences were observed with the md parameters, the gromacs version and finally how the charge group distribution to compute the force during the simulations. http://hpics.li/9ed5ee1 -- Secondary structure vs. time http://hpics.li/7cf1625 -- RMSD vs. time So i suspect that the errors come from the use a bad version of the CHARMM27 ff Thank you all for your preceding comments SA Francesco Oteri wrote: To see if the problem is force-field related, you could try to run the same simulations using amber-ff. If you will find the same results, probably is a software bug. Some Amber parameter sets (Amber94, I think) have issues of being overly helix-friendly, but perhaps other force fields, in general, might make for good comparisons. But then, too, Gromos96 over-stabilizes extended conformations, so buyer beware... Maybe the bug has been introduced in the version 4 when the Domain Decomposition has been introduced. You can check if it is a software problem using the 3.3.3 version. I doubt that would work. There have been many code changes in order to implement CHARMM. If anything, try mdrun -pd to use the old particle decomposition mode, but I would be very hesitant to blindly say that DD might be causing this behavior. -Justin Il 25/11/2010 23:42, sa ha scritto: Dear All, In a previous message (http://lists.gromacs.org/pipermail/gmx-users/2010-November/055839.html ), I described the results obtained with MD performed with the CHARMM27 ff and the chargegrp yes and no options of a peptide in TIP3P water simulated gromacs. Since these results puzzled me a lot, i would like to share with you others results obtained from the gromacs community advices to explain these results. In few words, the context of these simulations. One of my labmate did, 8 months ago (march/april), several simulations of a peptide (25 AA) with the CHARMM27 ff (and CMAP). The peptide is a transmembrane segment (TM) and belongs to a large membrane protein. This TM segment has an initial helical conformation. The simulations were performed in a cubic box filled with app. 14000 TIP3P water (Jorgensen's model) with 2 Cl ions. To construct the topology file of the system, -chargegrp yes with pdb2gmx and the MD were done with the gromacs 4.0.5. For some reasons, he had to left the lab, and my boss asked me to continue his work. When I checked their results, i was very intrigued by these MD results because he found that the peptide keep along all the simulation time (100 ns) its initial helical conformation. This results are not in agreement with circular dichroism experiments which are shown that the same peptide in water has no helix segment and is completely unfold. I am aware that the simulation time is short compared to experiment time scale, however since i haven't seen any unfolding events in this simulation, so I was not very confident about these results. To explain this inconsistency, I have suspected that the error came probably of the use
[gmx-users] Re: gmx-users Digest, Vol 79, Issue 167
Hi Tom. Hi, You show differences when using GROMACS 4.5.3 for one simulation with the pdb2gmx option -nochargegrp and one without this option (is this correct, or did you manually edit the topology to have the old charge groups?). This pdb2gmx option should have no effect in 4.5.3 as all the entries in the CHARMM27 .rtp are in individual charge groups. I will try to be more clear here: First step: The two top files were generated with different rtp files. In the first case i used a rtp file where the charge groups for each AA were distributed as in the CHARMM27 ff distribution. The top file were generated the gromacs (4.0.5) and the following command pdb2gmx_mpi -ignh -ff charmm27 -ter -f hMRP1_K-TM17_AcAm.pdb -o hMRP1_K-TM17.gro -p hMRP1_K-TM17.top -missing For the second top i used gromacs 4.5 with the argument -nochargegrp (with one charge group assigned for atom) with the command pdb2gmx_mpi -ignh -ff charmm27 -ter -f hMRP1_K-TM17_AcAm-H.pdb -o hMRP1_K-TM17.gro -p hMRP1_K-TM17.top -missing -nochargegrp Second Step: i used the latest version of gromacs 4.5.3 to generate the different tpr files and performed the simulations with the two types of top files. In case of the MD with the others versions of gromacs, the step two was done with the cooresponding version of gromacs. If you didn't edit the 4.5.3 topology then either you are doing something else different between these simulations or what you think is a difference between simulations with and without this pdb2gmx option is just a coincidence and that your peptide is sometimes stable over this short 24 ns simulation and sometimes it unfolds, irrespective of the charge group option. I have also performed a MD during 100 ns (with -chargegroup), and in this case the peptide remains stable along the simulation time. I don't understand why. Moreover i dont think it is a coincidence since i observe the same results whatever the gmx version and md parameters used If you did edit the topology then are you sure that it is correct? Did you use 4.5.3 to get the topology and edit it by hand or did you generate this 'charge group' topology by some other method, such as another version of GROMACS? If you used the topology from 4.0.x then maybe there are issues here as I know CHARMM27 was not fully supported until 4.5. I didn't edit the top file manually, i used only the pdb2gmx tool. However by reading your message, i have take a look more deeper in te the top file and i have found differences in some directives (for example in the pair directive where there are more terms). =-O To be sure that this difference has no impact in the MD, i going to do other MD. I will come back soon. Thanks you again SA Cheers Tom On 25/11/10 22:42, sa wrote: Dear All, In a previous message (http://lists.gromacs.org/pipermail/gmx-users/2010-November/055839.html ), I described the results obtained with MD performed with the CHARMM27 ff and the chargegrp yes and no options of a peptide in TIP3P water simulated gromacs. Since these results puzzled me a lot, i would like to share with you others results obtained from the gromacs community advices to explain these results. In few words, the context of these simulations. One of my labmate did, 8 months ago (march/april), several simulations of a peptide (25 AA) with the CHARMM27 ff (and CMAP). The peptide is a transmembrane segment (TM) and belongs to a large membrane protein. This TM segment has an initial helical conformation. The simulations were performed in a cubic box filled with app. 14000 TIP3P water (Jorgensen's model) with 2 Cl ions. To construct the topology file of the system, -chargegrp yes with pdb2gmx and the MD were done with the gromacs 4.0.5. For some reasons, he had to left the lab, and my boss asked me to continue his work. When I checked their results, i was very intrigued by these MD results because he found that the peptide keep along all the simulation time (100 ns) its initial helical conformation. This results are not in agreement with circular dichroism experiments which are shown that the same peptide in water has no helix segment and is completely unfold. I am aware that the simulation time is short compared to experiment time scale, however since i haven't seen any unfolding events in this simulation, so I was not very confident about these results. To explain this inconsistency, I have suspected that the error came probably of the use of the default -chargegrp with CHARMM ff in these simulations since i have read several recent threads about the charge groups problems in the CHARMM ff implementation in gromacs. To examine this hypothesis I have done two simulations with last gromacs version (4.5.3) and two top files containing charge groups and no charge groups for the peptide residus. I used the *same* initial pdb file, box size and simulations parameters. The two simulations
[gmx-users] Discrepancy between -chargegrp and -nochargegrp in simulations with CHARMM ff, Why ?
--- Potential -568520 24770.264 -165.498 (kJ/mol) Total Energy-463287 24955.755 -165.768 (kJ/mol) I am particularly eager to obtain from you some comments and advices about these findings. Thanks you so much for your help. SA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Spurious results with pdb2gmx -chargegrp yes option
Dear All, I would like to get little feedback of my findings/experience with recent simulations I did with the CHARMM force field in GROMACS and the -chargegroup options with pdb2gmx. I have performed two simulations with a helical peptide (25 AA) in a cubic box filled with explicit TIP3P water. I used the GMX 4.5.3. The first simulation was performed with -chargegroup option yes and the second with option no (default). For the first simulation, I used the old version of CHARMM - gromacs forcefield conversion given with GMX 4.0.5. I have done this MD because i would like to compare some suspect results obtained with the same peptide performed 6 months ago with the GMX 4.0.5 version and the old CHARMM-gromacs files available in this distribution. In case of the second simulation, I used the most recent charmm27.ff given in GMX 4.5.3 with a single atom charge groups. The two simulations were performed during 24 ns with the same protocol (i.e. with same mdp files, below and the same starting files). Briefly the protocol i used to equilibrate my system : EM (1000 steps with steep) - NVT at 298 K (with berendsen thermostat and restraints) (100 ps) - (with nose hoover thermostat and Parinello-Rahman barostat) 400 ps. Below md.mdp for the two runs ( i am aware that the Coulomb and electrostatic parameters in the mdp are not otimals for the CHARMM ff, but for sake of comparison with others simulations, i didn't change them). title = KTM17-TIP3 MD constraints = all-bonds integrator = md nsteps = 1200 ; 24000ps ou 24ns dt = 0.002 nstlist = 10 nstcalcenergy = 10 nstcomm = 10 continuation= no ; Restarting after NPT vdw-type= cut-off rvdw= 1.0 rlist = 0.9 coulombtype = PME rcoulomb = 0.9 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order= 4 ewald_rtol = 1e-05 optimize_fft= yes nstvout = 5 nstxout = 5 nstenergy = 2 nstlog = 5000 ; update log file every 2 ps nstxtcout = 1000 ; frequency to write coordinates to xtc trajectory every 2 ps Tcoupl = nose-hoover: tc-grps = Protein Non-Protein tau-t = 0.4 0.4 ref-t = 298 298 ; Pressure coupling is on Pcoupl = Parrinello-Rahman pcoupltype = isotropic tau_p = 3.0 compressibility = 4.5e-5 ref_p = 1.0135 gen_vel = no I found that the use of the two -chargegrp options influence drastically the MD results especially in my case for the structural properties of the peptides. Indeed, for the first simulation, the peptide keep in its initial helical with a RMSD around 2.0 A along all 24 ns, whereas in the second simulation, the peptide adopt quickly (~10 ns) a unfold conformation with a RMSD value around 5-6.0 A after only 10 ns. Circular dichroism experiments have shown that this peptide adopt an unfold structure in water. So I am sure that the first simulation is not correct (even if the mdp parameters are not optimal) and that my results confirm that chargegrp yes option should not be used in MD with CHARMM force field in GROMACS, as it was discussed recently in this mailing list (for example http://lists.gromacs.org/pipermail/gmx-users/2010-September/054106.html). SA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_densmap options and use
Dear All, I would like to compute the average 2D density distribution of the water around 6 peptides aggregated in the cluster within the simulation box with gromacs, for that I think that g_densmap is the the good tool (correct ?). However it is not very clear for how to use g_densmap. Below the command I used with g_densmap (ver GMX 4.5.3) g_densmap_mpi -f ./TRAJ/XTC/6_Pep_Urea_Pref_All.xtc -s ./TRAJ/TPR/em.tpr -bin 0.02 -amax 30 -rmax 30 -b 0 -e 8 -o 6_Peptide_53A6_densmap.xpm -od 6_Peptide_53A6_densmap.dat When I use the above command, g_densmap asks me to choose two groups to define the axis and an analysis group: Reading file ./TRAJ/TPR/em.tpr, VERSION 4.5.1 (single precision) Reading file ./TRAJ/TPR/em.tpr, VERSION 4.5.1 (single precision) Select two groups to define the axis and an analysis group Group 0 ( System) has 86359 elements Group 1 (Protein) has 546 elements Group 2 ( Protein-H) has 396 elements Group 3 (C-alpha) has48 elements Group 4 ( Backbone) has 144 elements Group 5 ( MainChain) has 192 elements Group 6 ( MainChain+Cb) has 234 elements Group 7 (MainChain+H) has 246 elements Group 8 ( SideChain) has 300 elements Group 9 (SideChain-H) has 204 elements Group10 (Prot-Masses) has 546 elements Group11 (non-Protein) has 85813 elements Group12 ( Other) has 17320 elements Group13 (URE) has 17320 elements Group14 ( CL) has 6 elements Group15 ( Water) has 68487 elements Group16 (SOL) has 68487 elements Group17 ( non-Water) has 17872 elements Group18 (Ion) has 6 elements Group19 (URE) has 17320 elements Group20 ( CL) has 6 elements Group21 ( Water_and_ions) has 68493 elements Select a group: 1 Selected 1: 'Protein' Select a group: 16 Selected 16: 'SOL' Select a group: 16 Selected 16: 'SOL' I chose protein and SOL, the program ask me to choose a third group (?) What to choose ? I choose SOL again, the program computes something but i can not inspect the results are what i want since no xpm is generated by g_densmap (is this a bug ?) Thank you for your help and your guidance Stefane -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: gmx-users Digest, Vol 79, Issue 88
On 13/11/2010 4:07 AM, sa wrote: Dear All, I would like to compute the average 2D density distribution of the water around 6 peptides aggregated in the cluster within the simulation box with gromacs, for that I think that g_densmap is the the good tool (correct ?). However it is not very clear for how to use g_densmap. Below the command I used with g_densmap (ver GMX 4.5.3) g_densmap_mpi -f ./TRAJ/XTC/6_Pep_Urea_Pref_All.xtc -s ./TRAJ/TPR/em.tpr -bin 0.02 -amax 30 -rmax 30 -b 0 -e 8 -o 6_Peptide_53A6_densmap.xpm -od 6_Peptide_53A6_densmap.dat When I use the above command, g_densmap asks me to choose two groups to define the axis and an analysis group: Reading file ./TRAJ/TPR/em.tpr, VERSION 4.5.1 (single precision) Reading file ./TRAJ/TPR/em.tpr, VERSION 4.5.1 (single precision) Select two groups to define the axis and an analysis group Group 0 ( System) has 86359 elements Group 1 (Protein) has 546 elements Group 2 ( Protein-H) has 396 elements Group 3 (C-alpha) has48 elements Group 4 ( Backbone) has 144 elements Group 5 ( MainChain) has 192 elements Group 6 ( MainChain+Cb) has 234 elements Group 7 (MainChain+H) has 246 elements Group 8 ( SideChain) has 300 elements Group 9 (SideChain-H) has 204 elements Group10 (Prot-Masses) has 546 elements Group11 (non-Protein) has 85813 elements Group12 ( Other) has 17320 elements Group13 (URE) has 17320 elements Group14 ( CL) has 6 elements Group15 ( Water) has 68487 elements Group16 (SOL) has 68487 elements Group17 ( non-Water) has 17872 elements Group18 (Ion) has 6 elements Group19 (URE) has 17320 elements Group20 ( CL) has 6 elements Group21 ( Water_and_ions) has 68493 elements Select a group: 1 Selected 1: 'Protein' Select a group: 16 Selected 16: 'SOL' Select a group: 16 Selected 16: 'SOL' I chose protein and SOL, the program ask me to choose a third group (?) What to choose ? Doesn't g_densmap -h explain the three groups? Yes I have read the help of the tool but it is not clear to me why i have to choose three groups since i want to compute the water density map around my peptides (- two groups) I choose SOL again, the program computes something but i can not inspect the results are what i want since no xpm is generated by g_densmap (is this a bug ?) Probably badly-formed input is silently breaking something somewhere. I don't understand your response since with the above command and -o argument show that an xpm with the name 6_Peptide_53A6_densmap.xpm should appear :-) G R O M A C S (-: Gnomes, ROck Monsters And Chili Sauce :-) VERSION 4.5.3 (-: Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff, Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, Michael Shirts, Alfons Sijbers, Peter Tieleman, Berk Hess, David van der Spoel, and Erik Lindahl. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2010, The GROMACS development team at Uppsala University The Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) /work/taulier01/gromacs-4.5.3/bin/g_densmap_mpi (-: Option Filename Type Description -f ./TRAJ/XTC/6_Pep_Urea_Pref_All.xtc InputTrajectory: xtc trr trj gro g96 pdb cpt -s ./TRAJ/TPR/em.tpr Input, Opt! Structure+mass(db): tpr tpb tpa gro g96 pdb -n index.ndx Input, Opt. Index file -od 6_Peptide_53A6_densmap.dat Output, Opt! Generic data file -o 6_Peptide_53A6_densmap.xpm Output X PixMap compatible matrix file Stefane Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http
[gmx-users] Re: gmx-users Digest, Vol 79, Issue 89
sa wrote: On 13/11/2010 4:07 AM, sa wrote: Dear All, I would like to compute the average 2D density distribution of the water around 6 peptides aggregated in the cluster within the simulation box with gromacs, for that I think that g_densmap is the the good tool (correct ?). However it is not very clear for how to use g_densmap. Below the command I used with g_densmap (ver GMX 4.5.3) g_densmap_mpi -f ./TRAJ/XTC/6_Pep_Urea_Pref_All.xtc -s ./TRAJ/TPR/em.tpr -bin 0.02 -amax 30 -rmax 30 -b 0 -e 8 -o 6_Peptide_53A6_densmap.xpm -od 6_Peptide_53A6_densmap.dat When I use the above command, g_densmap asks me to choose two groups to define the axis and an analysis group: Reading file ./TRAJ/TPR/em.tpr, VERSION 4.5.1 (single precision) Reading file ./TRAJ/TPR/em.tpr, VERSION 4.5.1 (single precision) Select two groups to define the axis and an analysis group Group 0 ( System) has 86359 elements Group 1 (Protein) has 546 elements Group 2 ( Protein-H) has 396 elements Group 3 (C-alpha) has48 elements Group 4 ( Backbone) has 144 elements Group 5 ( MainChain) has 192 elements Group 6 ( MainChain+Cb) has 234 elements Group 7 (MainChain+H) has 246 elements Group 8 ( SideChain) has 300 elements Group 9 (SideChain-H) has 204 elements Group10 (Prot-Masses) has 546 elements Group11 (non-Protein) has 85813 elements Group12 ( Other) has 17320 elements Group13 (URE) has 17320 elements Group14 ( CL) has 6 elements Group15 ( Water) has 68487 elements Group16 (SOL) has 68487 elements Group17 ( non-Water) has 17872 elements Group18 (Ion) has 6 elements Group19 (URE) has 17320 elements Group20 ( CL) has 6 elements Group21 ( Water_and_ions) has 68493 elements Select a group: 1 Selected 1: 'Protein' Select a group: 16 Selected 16: 'SOL' Select a group: 16 Selected 16: 'SOL' I chose protein and SOL, the program ask me to choose a third group (?) What to choose ? Doesn't g_densmap -h explain the three groups? Yes I have read the help of the tool but it is not clear to me why i have to choose three groups since i want to compute the water density map around my peptides (- two groups) The first two groups determine the axis. Per g_densmap -h: Three groups should be supplied, the centers of mass of the first two groups define the axis, the third defines the analysis group. I suspect the fact that you've chosen SOL for the second group might be causing problems (since, presumably, you have water all around), but I have never used g_densmap, so I don't know for sure. -Justin Ok I will try and play with the different groups of my system to see if it works... Stefane I choose SOL again, the program computes something but i can not inspect the results are what i want since no xpm is generated by g_densmap (is this a bug ?) Probably badly-formed input is silently breaking something somewhere. I don't understand your response since with the above command and -o argument show that an xpm with the name 6_Peptide_53A6_densmap.xpm should appear :-) G R O M A C S (-: Gnomes, ROck Monsters And Chili Sauce :-) VERSION 4.5.3 (-: Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff, Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, Michael Shirts, Alfons Sijbers, Peter Tieleman, Berk Hess, David van der Spoel, and Erik Lindahl. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2010, The GROMACS development team at Uppsala University The Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) /work/taulier01/gromacs-4.5.3/bin
[gmx-users] Problems with NVT simulation with CHARMM27
-14795599.0003.894 Old cell boundaries in direction Y:4.3719.400 New cell boundaries in direction Y:4.3709.400 Step 1500: The charge group starting at atom 47947 moved than the distance allowed by the domain decomposition (1.20) in direction Y distance out of cell 19727472.00 Old coordinates:5.5304.4192.912 New coordinates: -11100299.000 19727476.0005.506 Old cell boundaries in direction Y:0.0004.579 New cell boundaries in direction Y:0.0004.585 - I aware that these errors are probably caused by a system not well equilibrated but since the Steepest Descents minimization are well converged, i am puzzled for the NVT simulation. I have checked the parameters of the force field and for me they are corrects, tried several protocols (reduce the time step (2 -1 fs, above, lower the temperature, or increase the number of minimization steps, etc.) with no success. Any advices will be greatly appreciated. Thank you for your help. sa -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
