[gmx-users] Umbrella Sampling continuation
Lalita Shaki
lalitashaky at gmail.com
Thu Dec 4 11:35:22 CET 2014
Dear Alexander,
As you used -deffnm umbrella0, you should have a file umbrella0.cpt insted
of state.cpt which allows you to restart the calculation.
Regards,
lalita
On Thu, Dec 4, 2014 at 10:17 AM, <
gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:
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> Today's Topics:
>
> 1. Re: use of g_hbond (Alexander Law)
> 2. Umbrella Sampling continuation (Alexander Law)
> 3. Errors about dihidral angle type 9 in free energy
> perturbation (Jianguo Li)
> 4. Errors about dihidral angle type 9 in free energy
> perturbation (Jianguo Li)
> 5. g_spatial (pratibha kapoor)
> 6. energy groups rerun from reduced xtc file (Harry Mark Greenblatt)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 04 Dec 2014 07:02:14 +0000
> From: Alexander Law <alexander.law at pg.canterbury.ac.nz>
> To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] use of g_hbond
> Message-ID:
> <
> F1F88268A76CB24687490BEE4249441B5F6A77F0 at UCEXMBX03-I.canterbury.ac.nz>
>
> Content-Type: text/plain; charset=us-ascii
>
> Ignore message, didn't read correctly
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of soumadwip
> ghosh [soumadwipghosh at gmail.com]
> Sent: Thursday, December 04, 2014 7:25 PM
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] use of g_hbond
>
> Hello everyone,
> I want to calculate the effect of incorporating
> ions in the grooves and backbones of a double stranded DNA molecule in the
> hydrogen bonding between the two chains constituting the DNA. I want to
> calculate the number, distance distribution and the lifetime of H- bonding
> between base pairs of two chains both in presence and in absence of the
> sodium ion. As far as I know, from the g_hbond utility of GROMACS we can
> calculate the hydrogen bond related parameters but I am not quite sure with
> the indexing. My index group looks like-
>
> Group 0 ( System) has 97135 elements
> Group 1 ( DNA) has 758 elements
> Group 2 ( NA) has 624 elements
> Group 3 ( CL) has 602 elements
> Group 4 ( Water) has 95151 elements
> Group 5 ( SOL) has 95151 elements
> Group 6 ( non-Water) has 1984 elements
> Group 7 ( Ion) has 1226 elements
> Group 8 ( NA) has 624 elements
> Group 9 ( CL) has 602 elements
> Group 10 ( Water_and_ions) has 96377 elements
> Group 11 ( major) has 376 elements
> Group 12 ( minor) has 256 elements
> Group 13 ( chain_A) has 379 elements
> Group 14 ( chain_B) has 379 elements
> Group 15 ( chain_A_Na) has 1 elements
> Group 16 (chain_A_chain_A_Na) has 380 elements
> Group 17 ( backbone) has 258 elements
>
> I decomposed the entire DNA molecule into two segments, chain_A and chain_B
> so that I can calculate the H-bonding parameters between the two chains.
> But I dont know what to do when I want to check the H-bonding between
> chain_A and chain_B in presence of sodium. Should I make a separate group
> of chainA and Na (say chain_A_Na) and then calculate the h-bonding with
> chain_B? Am I doing anything wrong? Is it supposed to be done in some other
> ways? Please help me out with this.Thanks in advance.
>
> Regards,
> Soumadwip Ghosh
> Senior research fellow,
> Indian Institute of Technology, Bombay
> India.
> --
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> ------------------------------
>
> Message: 2
> Date: Thu, 04 Dec 2014 04:12:56 +0000
> From: Alexander Law <alexander.law at pg.canterbury.ac.nz>
> To: "gromacs.org_gmx-users at maillist.sys.kth.se"
> <gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: [gmx-users] Umbrella Sampling continuation
> Message-ID:
> <
> F1F88268A76CB24687490BEE4249441B5F6A77CA at UCEXMBX03-I.canterbury.ac.nz>
>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear gmx-users
>
> I am running umbrella sampling and running the last simulations before
> analysis using this command:
>
>
> mdrun -deffnm umbrella0 -pf pullf-umbrella0.xvg -px pullx-umbrella0.xvg
>
> Some of my simulations have crashed before completion and I wish to
> continue them, in the past I have used the state.cpt file, but this doesn't
> seem to be an option for this type of simulation as the file is not
> produced. Is there an alternative method?
>
> Thanks,
>
> Alex
>
> This email may be confidential and subject to legal privilege, it may
> not reflect the views of the University of Canterbury, and it is not
> guaranteed to be virus free. If you are not an intended recipient,
> please notify the sender immediately and erase all copies of the message
> and any attachments.
>
> Please refer to http://www.canterbury.ac.nz/emaildisclaimer for more
> information.
>
>
> ------------------------------
>
> Message: 3
> Date: Thu, 4 Dec 2014 07:32:56 +0000 (UTC)
> From: Jianguo Li <ljggmx at yahoo.com.sg>
> To: "gromacs.org_gmx-users at maillist.sys.kth.se"
> <gromacs.org_gmx-users at maillist.sys.kth.se>,
> "gromacs.org_gmx-users at maillist.sys.kth.se"
> <gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: [gmx-users] Errors about dihidral angle type 9 in free energy
> perturbation
> Message-ID:
> <
> 721959541.2530443.1417678376233.JavaMail.yahoo at jws10945.mail.sg3.yahoo.com
> >
>
> Content-Type: text/plain; charset=UTF-8
>
> Dear All,
> I am trying to use free energy perturbation module of gromacs to do
> hamiltonian replica exchange using CHARMM27 all-atom force field (with
> CMAP) - version 2.0
>
> I am using 4.5.4 version of gromacs
>
> according to manual (Table 5.5), it allows to perturb dihedral angles:
> proper dih. multi,? ftp 9, phi and k are allowed under 'F.E.'
>
> I have edited charmm files( ffbonded.itp and also ffnonbonded.itp) for
> "state B" parameters.
> but when I run simulations, it throws following error (for 23 lines):
> "
> ERROR 1 [file topol-edited-charmm.top, line 1453]:
> ? Cannot automatically perturb a torsion with multiple terms to different
> ? form.
> ? Please specify perturbed parameters manually for this torsion in your
> ? topology!
> "
>
> What is the fix for this?
> Why gromacs is not recognising the 'state B' parameters?
>
> I also tried to do this with higher version of gromacs (including latest).
> It throws the same error.
>
>
> Thank you very much for your time.
>
> Cheers,Jianguo
>
>
>
> ------------------------------
>
> Message: 4
> Date: Thu, 4 Dec 2014 07:32:56 +0000 (UTC)
> From: Jianguo Li <ljggmx at yahoo.com.sg>
> To: "gromacs.org_gmx-users at maillist.sys.kth.se"
> <gromacs.org_gmx-users at maillist.sys.kth.se>,
> "gromacs.org_gmx-users at maillist.sys.kth.se"
> <gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: [gmx-users] Errors about dihidral angle type 9 in free energy
> perturbation
> Message-ID:
> <
> 721959541.2530443.1417678376233.JavaMail.yahoo at jws10945.mail.sg3.yahoo.com
> >
>
> Content-Type: text/plain; charset=UTF-8
>
> Dear All,
> I am trying to use free energy perturbation module of gromacs to do
> hamiltonian replica exchange using CHARMM27 all-atom force field (with
> CMAP) - version 2.0
>
> I am using 4.5.4 version of gromacs
>
> according to manual (Table 5.5), it allows to perturb dihedral angles:
> proper dih. multi,? ftp 9, phi and k are allowed under 'F.E.'
>
> I have edited charmm files( ffbonded.itp and also ffnonbonded.itp) for
> "state B" parameters.
> but when I run simulations, it throws following error (for 23 lines):
> "
> ERROR 1 [file topol-edited-charmm.top, line 1453]:
> ? Cannot automatically perturb a torsion with multiple terms to different
> ? form.
> ? Please specify perturbed parameters manually for this torsion in your
> ? topology!
> "
>
> What is the fix for this?
> Why gromacs is not recognising the 'state B' parameters?
>
> I also tried to do this with higher version of gromacs (including latest).
> It throws the same error.
>
>
> Thank you very much for your time.
>
> Cheers,Jianguo
>
>
>
> ------------------------------
>
> Message: 5
> Date: Thu, 4 Dec 2014 14:17:13 +0530
> From: pratibha kapoor <kapoorpratibha7 at gmail.com>
> To: gmx-users at gromacs.org
> Subject: [gmx-users] g_spatial
> Message-ID:
> <
> CAPzRJV0Fc5K_grip_UkkQud+gZRv2DAnMEriJKj7MDeZaQqx-w at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi,
>
> I would like to calculate spatial distribution function of my cosolvent
> molecules around peptides. I am using g_spatial tool. I have removed
> periodicity, rotational and translational motion of my solute as suggested
> in the manual. grid.cube file was generated after using g_spatial command.
> But when I set isosurface under the drawing method in vmd, I could see
> nothing. How to visualise it?
>
> Thanks
>
>
> ------------------------------
>
> Message: 6
> Date: Thu, 4 Dec 2014 09:16:56 +0000
> From: Harry Mark Greenblatt <harry.greenblatt at weizmann.ac.il>
> To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> Subject: [gmx-users] energy groups rerun from reduced xtc file
> Message-ID: <8F1D5C48-6E39-4000-AFFA-95287431F101 at weizmann.ac.il>
> Content-Type: text/plain; charset="us-ascii"
>
> BS"D
>
> Dear All,
>
> In an attempt to save disk space while using longer simulations of a
> DNA + Protein + solvent system,
> I had mdrun create an xtc file with only the DNA, Protein, and ions,
> excluding the water molecules.
> No trr file was produced. This is fine for many things, but since I also
> want to look at energies between
> defined groups, and the GPU-based calculations do not support this, I need
> to to a "rerun" of the simulation with CPU's only,
> to do the energy calculations.
>
> If I understood correctly, the procedure to change or introduce energy
> groups would be:
>
> grompp -f yournew.mdp -c yourold.gro -t yourold.cpt -p your.top -o
> newrerun.tpr -n yournewindexfile.ndx
>
> mdrun -v -s newrerun.tpr -rerun yourold.xtc -e new.edr
>
> The problem is that the xtc file and the initial topology no longer have
> the same number of atoms. I have gone through a lot of conversions,
> to create new top and gro files without water molecules.
>
> I was not, however, able to take care of cpt file, since my attempt to use
> trjconv succeeded, but grompp does not like it because trjconv
> does not output a cpt file.
>
> Is there a solution to this problem (other than having to produce all-atom
> xtc or trr files)?
>
> Thanks
>
> Harry
>
>
>
>
>
> -------------------------------------------------------------------------
>
> Harry M. Greenblatt
>
> Associate Staff Scientist
>
> Dept of Structural Biology
>
> Weizmann Institute of Science Phone: 972-8-934-3625
>
> 234 Herzl St. Facsimile: 972-8-934-4159
>
> Rehovot, 76100
>
> Israel
>
>
> Harry.Greenblatt at weizmann.ac.il<mailto:Harry.Greenblatt at weizmann.ac.il>
>
>
>
>
>
>
>
>
>
> ------------------------------
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
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> send a mail to gmx-users-request at gromacs.org.
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>
> End of gromacs.org_gmx-users Digest, Vol 128, Issue 16
> ******************************************************
>
--
Lalita S. Uribe.
European Master in Theoretical Chemistry and Computational Modeling.
PhD student. Johannes Gutenberg-Universität Mainz
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