[gmx-users] error in running mdrun of membrane protein in a mixed bilayer with MARTINI MODEL
Justin Lemkul
jalemkul at vt.edu
Sun May 15 14:14:11 CEST 2016
Please don't reply to entire digests.
On 5/15/16 4:48 AM, Antara mazumdar wrote:
> Dear Justin,
>
> I am using the velocities from the NPT run. Could you please explain on the
> .cpt file you mentioned?
>
This command:
gmx grompp -c step6.6equilibration.gro -p system.top -n new_index.ndx -f
MD.mdp -o MD.tpr
might preserve the low-precision velocities written to the .gro file, but it
preserves nothing about the ensemble at the end of the equilibration run.
Consult any basic tutorial for proper usage of grompp and continuing runs. If
you don't carefully continue your simulations, you're going to find all sorts of
bizarre behavior.
-Justin
> Kind Regards,
> Antara
>
> --
> Junior research fellow(project)
> Systems biology group
> CSIR-Institute of Genomics & Integrative Biology
> South Campus
> New Delhi - 110020
> M : +91-9717970040
> --
>
>
>
> On Sun, May 15, 2016 at 10:51 AM, <
> gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:
>
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>> Today's Topics:
>>
>> 1. COM-Pull along a direction (Pengzhi Zhang)
>> 2. Re: error in running mdrun of membrane protein in a mixed
>> bilayer with MARTINI MODEL (Justin Lemkul)
>> 3. Umbrella Sampling - choice of pull-coord?-dim (Lukas Zimmermann)
>> 4. PCA and FEL (sun)
>> 5. Re: PCA and FEL (Tsjerk Wassenaar)
>>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Sat, 14 May 2016 14:58:37 -0500
>> From: Pengzhi Zhang <pzhang5 at central.uh.edu>
>> To: <gromacs.org_gmx-users at maillist.sys.kth.se>
>> Subject: [gmx-users] COM-Pull along a direction
>> Message-ID: <5737836D.8010409 at central.uh.edu>
>> Content-Type: text/plain; charset="utf-8"; format=flowed
>>
>> Dear Gromacs users,
>>
>> I am trying to pull an ion out of a protein using Gromacs/5.0.4. I pull
>> the ion along specific pre-determined paths.
>>
>> From my understanding, pulling along a direction _V guarantees that the
>> dumb bead would move only at direction _V. The position of the dumb bead
>> is simply: _r(t) = _r(0) + _V*speed*time (_ means vector). And if the
>> spring constant is sufficiently large, the pulled atom (a single ion)
>> would also follow the dumb bead (with fluctuations). However, I found
>> that no matter how large the spring constant is (I vary it from 100 to
>> 1,000,000 kJ/mol/nm**2), the pulled atom deviates from the direction _V
>> in a certain amount of time (usually after the pulled bead unbinds),
>> sometimes it even goes perpendicular to _V and moves out of the box,
>> terminating the simulation.
>>
>> Does the direction _V (pull-coord1-vec) mean the direction of
>> instantaneous pull force or the direction of the path that the dumb bead
>> follows?
>>
>> Thank you very much in advance!
>>
>>
>> Here is the pull part of my mdp file.
>> ; COM PULLING
>> ; Pull type: no, umbrella, constraint or constant-force
>> pull = umbrella
>> pull-geometry = direction
>> pull-ngroups = 2
>> pull-ncoords = 1
>> pull-group1-name = binding_site_atoms
>> pull-group2-name = pull_ion ; pull group
>> pull-start = yes
>> pull-coord1-vec = -0.07 -0.04 0.99
>> pull-coord1-groups = 1 2
>> pull_coord1_rate = 0.001 ; nm/ps
>> pull-coord1-k = 10000 ; kJ/mol/nm^2
>> pull-nstxout = 10 ; 0.02 ps
>> pull-nstfout = 10
>> pull-print-reference = yes
>>
>>
>> Sincerely,
>> Pengzhi
>>
>>
>> ------------------------------
>>
>> Message: 2
>> Date: Sat, 14 May 2016 18:33:08 -0400
>> From: Justin Lemkul <jalemkul at vt.edu>
>> To: gmx-users at gromacs.org
>> Subject: Re: [gmx-users] error in running mdrun of membrane protein in
>> a mixed bilayer with MARTINI MODEL
>> Message-ID: <5b732333-0517-e66f-2e4b-7a9cf337e3d9 at vt.edu>
>> Content-Type: text/plain; charset=windows-1252; format=flowed
>>
>>
>>
>> On 5/14/16 2:34 PM, Mark Abraham wrote:
>>> Hi,
>>>
>>> Please keep the discussion on the mailing list, so others can help and
>>> learn.
>>>
>>>> Antara said:
>>>> I have pasted the mdrun command i used to run it in parallel with the
>>> number of processors i used which was 16. The command is :
>>>>
>>>>
>>>> /app/setups/gromacs-5.1.1/build/bin -deffnm MD -pin on -rdd 1.8
>>>
>>> That still isn't a command you've copied and pasted from a terminal or a
>>> script. You needed a call that might include mpirun -np 16 gmx_mpi mdrun,
>>> etc.
>>>
>>>> In the pbs script, i used 16 in the number of processors option.
>>>
>>> What happens when you run on one rank?
>>>
>>>> For the production tpr, i used the gro file from the last equilibration
>>> step(step6.6) The command used was :
>>>>
>>>> gmx grompp -c step6.6equilibration.gro -p system.top -n new_index.ndx -f
>>> MD.mdp -o MD.tpr
>>>
>>> That looks like it could be reasonable, but as with any equilibration you
>>> need to look at observables to judge that it's equilibrated. Their
>> builder
>>> should provide reasonable defaults, but you can't assume they're perfect,
>>> either. In particular, if the last equilibration ensemble doesn't match
>> the
>>> production ensemble, that could be the problem.
>>>
>>
>> Failing to pass the .cpt file to grompp -t after equilibration is a great
>> way to
>> do that. The production simulation is starting from some unpredictable
>> ensemble, without velocities, etc..
>>
>> -Justin
>>
>>> Mark
>>>
>>> On Sat, May 14, 2016 at 5:10 PM Mark Abraham <mark.j.abraham at gmail.com>
>>> wrote:
>>>
>>>> Hi,
>>>>
>>>> On Sat, May 14, 2016 at 4:34 PM Antara mazumdar <
>> antara.mazumdar at igib.in>
>>>> wrote:
>>>>
>>>>> Dear users,
>>>>>
>>>>> I am trying to run a coarse grained simulation of a membrane protein
>> in a
>>>>> mixed lipid billayer using martini model 2.2. I have already performed
>> all
>>>>> the equilibration steps successfully on my desktop with GROMACS 5.1.0.
>>>>> However, when i try to execute its production run in parallel(having
>>>>> gromacs 5.1 version installed) it complains of LINCS warning and
>>>>> terminates at step 0. The lincs warning error is coming from BB and SC1
>>>>> atoms of one of the protein residues.
>>>>>
>>>>
>>>> There are lots of possible places to go wrong, including not making your
>>>> production .tpr based on the outputs of your equilibration. This seems
>>>> quite a likely possibility.
>>>>
>>>> You should also consider further equilibration - whether using Martini
>> or
>>>> not, it is sometimes necessary to use a small time step when relaxing
>>>> problem configurations.
>>>>
>>>>
>>>>> But on the contrary, it runs on the desktop successfully. *My
>> production
>>>>> run mdp file details are below :*
>>>>>
>>>>>
>>>>> .
>>>>>
>>>>> This is the MD.mdp file :ntegrator = md
>>>>> tinit = 0.0
>>>>> dt = 0.020
>>>>> nsteps = 2500000000
>>>>>
>>>>> nstxout = 2000
>>>>> nstvout = 2000
>>>>> nstfout = 2000
>>>>> nstlog = 2000
>>>>> nstenergy = 2000
>>>>> nstxtcout = 2000
>>>>> xtc_precision = 100
>>>>>
>>>>> ns_type = grid
>>>>> pbc = xyz
>>>>> nstlist = 10
>>>>> cutoff-scheme = Verlet
>>>>> rlist = 1.2
>>>>> vdwtype = Cut-off
>>>>> vdw-modifier = none
>>>>> rvdw_switch = 1.0
>>>>> rvdw = 1.2
>>>>> coulombtype = pme
>>>>> rcoulomb = 1.2
>>>>>
>>>>> tcoupl = v-rescale
>>>>> tc-grps = protein CHOL_POPC_DPSM_DPCE W_ION
>>>>>
>>>>> tau_t = 1.0 1.0 1.0
>>>>> ref_t = 303.15 303.15 303.15
>>>>>
>>>>> ; Pressure coupling:
>>>>> Pcoupl = berendsen
>>>>> Pcoupltype = semiisotropic
>>>>> tau_p = 5.0 5.0
>>>>> compressibility = 3e-4 3e-4
>>>>> ref_p = 1.0 1.0
>>>>> ; GENERATE VELOCITIES FOR STARTUP RUN:
>>>>> gen_vel = no
>>>>> refcoord_scaling = all
>>>>>
>>>>> *the command used for mdrun :*
>>>>>
>>>>> -deffnm MD -pin on -rdd 1.8 -np 16
>>>>>
>>>>
>>>> mdrun 5.1 won't accept -np, so I don't know what you are actually doing.
>>>> Please don't edit and filture things, copy and paste whole actual
>> things.
>>>> :-)
>>>>
>>>> Mark
>>>>
>>>> I would also like to mention that i generated the initial structure of
>> the
>>>>> system using CHARMM GUI MARTINI MAKER protein-membrane system option. I
>>>>> have followed the exact builder protocol for the equilibration and
>>>>> minimisation.
>>>>>
>>>>> Kindly suggest something!
>>>>>
>>>>> Thanks,
>>>>> Antara
>>>>>
>>>>> --
>>>>> Junior research fellow(project)
>>>>> Systems biology group
>>>>> CSIR-Institute of Genomics & Integrative Biology
>>>>> South Campus
>>>>> New Delhi - 110020
>>>>> M : +91-9717970040
>>>>> --
>>>>> --
>>>>> Gromacs Users mailing list
>>>>>
>>>>> * Please search the archive at
>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>>>> posting!
>>>>>
>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>>
>>>>> * For (un)subscribe requests visit
>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>>>> send a mail to gmx-users-request at gromacs.org.
>>>>>
>>>>>
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 629
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==================================================
>>
>>
>> ------------------------------
>>
>> Message: 3
>> Date: Sun, 15 May 2016 00:55:23 +0200
>> From: Lukas Zimmermann <luk.zim91 at gmail.com>
>> To: gromacs.org_gmx-users at maillist.sys.kth.se
>> Subject: [gmx-users] Umbrella Sampling - choice of pull-coord?-dim
>> Message-ID:
>> <CAPSKXTqEZw4=
>> 1CcAB3fTBPVTZFvRZLghz6D5eCQ1Yaq2yTgX4w at mail.gmail.com>
>> Content-Type: text/plain; charset=UTF-8
>>
>> Dear GROMACS users,
>>
>> I am interested in the role of the mdp parameter pull-coord?-dim when
>> sampling
>> a particular umbrella window after having generated initial configurations
>> for, say, the
>> COM distance between two groups being the reaction coordinate.
>>
>> I know that these options can be controlled to restrict the actual pulling,
>> say with geometry distance, to a subset of the pull vector components, for
>> instance to enable
>> aligment of the pull vector with the box dimensions.
>>
>> However, I do not understand its role when performing umbrella sampling
>> along the reaction coordinate.
>> I know that the pull-code then controls the COM distance between the pull
>> groups with a (usually) harmonic potential, but what effect will
>> pull-coord?-dim have?
>>
>> I observe different behavior for my toy system consisting of two methanol
>> molecules in vacuum.
>> With all components enables, I need to correct the PMF for entropic
>> decrease in the PMF,
>> since the methanol is sampled on a sphere with increasing radius.
>> If only allowing one component, the PMF will be flat, but different values
>> for delta G
>> result.
>>
>> Also, in the US Tutorial by Justin, the US code uses:
>>
>> pull_coord1_dim = N N Y
>>
>> Is there any particular reason, not to set
>>
>> pull_coord1_dim = Y Y Y
>>
>> here? Would this setting also be justified? Since, as far as I understood
>> the procedure, pulling
>>
>> is just there for generating the initial configurations and US is more or
>> less independent of this.
>>
>>
>>
>> Many thanks in advance!
>>
>> Lukas
>>
>>
>> ------------------------------
>>
>> Message: 4
>> Date: Sun, 15 May 2016 09:03:34 +0530
>> From: sun <sun.iba2 at gmail.com>
>> To: gmx-users at gromacs.org
>> Subject: [gmx-users] PCA and FEL
>> Message-ID: <EC81EF15-0FCC-4BA7-B3AA-84D789822105 at gmail.com>
>> Content-Type: text/plain; charset=us-ascii
>>
>> Hello everyone
>> I am using Gromacs 5.0 for protein-ligand MD. I want to do FEL analysis
>> for the stability of my pro-lig complex. In a 2015 paper, The group
>> calculated two principal component, PC1 and PC2 and then prepared an.xvg
>> file to be used as input for g_sham. My question is, when we use g_anaeig;
>> we get eigenvec.xvg. from -comp flag. Now how shall one select two
>> principal components from that data? I am sorry if my question is wrong but
>> please help me.
>>
>> My second question is, can we use any two parameters like rmsd and Rg for
>> input in g_sham to probe the stability of complex? Is that valid?
>>
>> With Regards
>> Suniba
>>
>> Sent from my iPhone
>>
>> ------------------------------
>>
>> Message: 5
>> Date: Sun, 15 May 2016 07:21:37 +0200
>> From: Tsjerk Wassenaar <tsjerkw at gmail.com>
>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> Subject: Re: [gmx-users] PCA and FEL
>> Message-ID:
>> <
>> CABzE1Sg4eZ1YtdBJsMC_Z-x3hOn3U1zqv74CoF4nSoaykss1BQ at mail.gmail.com>
>> Content-Type: text/plain; charset=UTF-8
>>
>> Hi Suniba,
>>
>> No, with gmx anaeig you can select -2d, which does a 2D projection onto the
>> selected eigenvectors. Alternatively, you can combine any two projections
>> onto eigenvectors, which you get using the option -proj. The quickest way
>> to do that is something like:
>>
>> paste <(grep -v '^[@#]' proj1.xvg) <(proj2.xvg) | awk '{print $2, $4}' >
>> combined.xvg
>>
>> You will loose the labels, but that should be fine.
>>
>> You can combine other variables in a similar manner.
>>
>> Hope it helps,
>>
>> Tsjerk
>>
>> On Sun, May 15, 2016 at 5:33 AM, sun <sun.iba2 at gmail.com> wrote:
>>
>>> Hello everyone
>>> I am using Gromacs 5.0 for protein-ligand MD. I want to do FEL analysis
>>> for the stability of my pro-lig complex. In a 2015 paper, The group
>>> calculated two principal component, PC1 and PC2 and then prepared an.xvg
>>> file to be used as input for g_sham. My question is, when we use
>> g_anaeig;
>>> we get eigenvec.xvg. from -comp flag. Now how shall one select two
>>> principal components from that data? I am sorry if my question is wrong
>> but
>>> please help me.
>>>
>>> My second question is, can we use any two parameters like rmsd and Rg for
>>> input in g_sham to probe the stability of complex? Is that valid?
>>>
>>> With Regards
>>> Suniba
>>>
>>> Sent from my iPhone
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>> posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-request at gromacs.org.
>>>
>>
>>
>>
>> --
>> Tsjerk A. Wassenaar, Ph.D.
>>
>>
>> ------------------------------
>>
>> --
>> 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.
>>
>> End of gromacs.org_gmx-users Digest, Vol 145, Issue 55
>> ******************************************************
>>
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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