[gmx-users] Velocity autocorrelation problem
Yutian Yang
yyang18 at syr.edu
Wed May 22 16:43:36 CEST 2013
Dear all,
I am trying to use g_velacc to calculate diffusion coefficient for a single polymer chain. As I follow the Gromacs tutorial and use the command (version 4.5.1)
g_velacc -acflen 1001 -nonormalize -mol -n atoms.ndx -s topol.tpr
the ACF is always zero. However, if I remove -mol option, the data shows up. It looks like -mol is a default option for the calculation so I don't know if it is still necessary to add it, or is it just a bug in the program?
Thank you!
Shirley
On May 22, 2013, at 10:31 AM, <gmx-users-request at gromacs.org>
wrote:
> Send gmx-users mailing list submissions to
> gmx-users at gromacs.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> or, via email, send a message with subject or body 'help' to
> gmx-users-request at gromacs.org
>
> You can reach the person managing the list at
> gmx-users-owner at gromacs.org
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of gmx-users digest..."
>
>
> Today's Topics:
>
> 1. Free energy of solvation's .mdp of peptide (maggin)
> 2. Re: MSD and frequency of writing trajectories (Erik Marklund)
> 3. Re: MSD and frequency of writing trajectories (Mark Abraham)
> 4. Re: error in running g_dist (Mark Abraham)
> 5. C6 & C12 parameters for non-bonded interactions using tables
> (Andrish Reddy)
> 6. Re: error in running g_dist (Andrish Reddy)
> 7. Re: C6 & C12 parameters for non-bonded interactions using
> tables (Mark Abraham)
> 8. COM coordinate fix (L.Liu at utwente.nl)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 22 May 2013 04:14:31 -0700 (PDT)
> From: maggin <maggin.chen at gmail.com>
> Subject: [gmx-users] Free energy of solvation's .mdp of peptide
> To: gmx-users at gromacs.org
> Message-ID: <1369221271481-5008445.post at n6.nabble.com>
> Content-Type: text/plain; charset=us-ascii
>
> Hi, if I want to calculate the free energy of solvation of peptide, because
> both van der Waals and Coulombic interactions are important for peptide
>
> so I set couple-lambda0 = none
> couple-lambda1 = vdw-q
>
> is it right?
>
> or it's better to choose wo-stage approach to do this work:
>
> van der Waals coupling:
>
> sc-alpha = 0.5 ; use soft-core for LJ (de)coupling
> sc-sigma = 0.3
> sc-power = 1
> couple-moltype = peptide
> couple-intramol = no
> couple-lambda0 = none ; non-interacting dummy in state A
> couple-lambda1 = vdw ; only vdW terms on in state B
> Coulombic coupling:
>
> sc-alpha = 0 ; soft-core during (dis)charging can be
> unstable!
> sc-sigma = 0
> couple-moltype = peptide
> couple-intramol = no
> couple-lambda0 = vdw ; only vdW terms in state A (the previous
> state B is now A)
> couple-lambda1 = vdw-q ; all nonbonded interactions are on in
> state B
>
> Thank you very much!
>
> maggin
>
>
>
>
>
>
> --
> View this message in context: http://gromacs.5086.x6.nabble.com/Free-energy-of-solvation-s-mdp-of-peptide-tp5008445.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 22 May 2013 13:17:41 +0200
> From: Erik Marklund <erikm at xray.bmc.uu.se>
> Subject: Re: [gmx-users] MSD and frequency of writing trajectories
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <1EFE1D47-497A-44FC-99B2-A8210D2C0726 at xray.bmc.uu.se>
> Content-Type: text/plain; charset=us-ascii
>
> Hi,
>
> For particles that diffuse more than half a box length between frames will appear as if they haven't moved much, assuming you have periodic boundary conditions.
>
> Erik
>
> On 22 May 2013, at 11:41, Anna Akinshina <anna.akinshina at manchester.ac.uk> wrote:
>
>> Dear Gromacs Users,
>>
>> I have a question interpreting obtained msd data.
>> I need to calculate diffusion coefficient for a single argon atom in a box of water (500 molecules).
>> During the calculations (50ns) I write both trr and xtc trajectories, but to save space I write trr for whole system very seldom (every 50000 steps = 100 ps)
>> but in xtc I have argon only (no water) and write more often (every 1000 steps = 2 ps).
>>
>> When I analysed the results using g_msd I was surprised that the msd curves obtained from trr and xtc trajectories differ a lot, what affect the resulting diffusion coefficients.
>>
>> If I save trr more often, like every 10000 steps (20ps) the results from both files coincide.
>>
>> Does the msd results depend on how often you write trajectories?
>> If yes, what frequency for writing the trajectories for future calculation of the diffusion coefficient would be reasonable and how long should be the calculations?
>>
>> Thanks you
>> Anna
>> -----------------------
>> Dr Anna Akinshina
>> School of Chemical Engineering & Analytical Science
>> The University of Manchester, UK
>>
>>
>> --
>> gmx-users mailing list gmx-users at 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-request at gromacs.org.
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
>
> ------------------------------
>
> Message: 3
> Date: Wed, 22 May 2013 13:19:50 +0200
> From: Mark Abraham <mark.j.abraham at gmail.com>
> Subject: Re: [gmx-users] MSD and frequency of writing trajectories
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
> <CAMNuMASM86_nMLFcXHezKR2TMMDAifwpRBnOgVhfOw+NxDvguA at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Sure. What's the MSD of a pendulum if you only sample at a rate equal to
> the period? How often you want to sample depends on the time scale of what
> you want to observe. That might be up to you to measure :-)
>
> Mark
>
>
> On Wed, May 22, 2013 at 11:41 AM, Anna Akinshina <
> anna.akinshina at manchester.ac.uk> wrote:
>
>> Dear Gromacs Users,
>>
>> I have a question interpreting obtained msd data.
>> I need to calculate diffusion coefficient for a single argon atom in a box
>> of water (500 molecules).
>> During the calculations (50ns) I write both trr and xtc trajectories, but
>> to save space I write trr for whole system very seldom (every 50000 steps =
>> 100 ps)
>> but in xtc I have argon only (no water) and write more often (every 1000
>> steps = 2 ps).
>>
>> When I analysed the results using g_msd I was surprised that the msd
>> curves obtained from trr and xtc trajectories differ a lot, what affect
>> the resulting diffusion coefficients.
>>
>> If I save trr more often, like every 10000 steps (20ps) the results from
>> both files coincide.
>>
>> Does the msd results depend on how often you write trajectories?
>> If yes, what frequency for writing the trajectories for future calculation
>> of the diffusion coefficient would be reasonable and how long should be the
>> calculations?
>>
>> Thanks you
>> Anna
>> -----------------------
>> Dr Anna Akinshina
>> School of Chemical Engineering & Analytical Science
>> The University of Manchester, UK
>>
>>
>> --
>> gmx-users mailing list gmx-users at 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-request at gromacs.org.
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>
>
> ------------------------------
>
> Message: 4
> Date: Wed, 22 May 2013 13:21:43 +0200
> From: Mark Abraham <mark.j.abraham at gmail.com>
> Subject: Re: [gmx-users] error in running g_dist
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
> <CAMNuMAQ_Vmbs1VYHhAwxExQ_9T6PnCvuMXa7wwf-WhHpj6-Dcw at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Use gmxcheck to find out what's in the files. Think about how you used
> xtcgroups. Consider using tpbconv to make a matching subset from your .tpr.
>
> Mark
>
>
> On Wed, May 22, 2013 at 11:53 AM, Arunima Shilpi <writetoash28 at gmail.com>wrote:
>
>> Respected sir
>>
>> I want to calculate the distance between protein and ligand after I have
>> run the production step. I used the following command..
>>
>> g_dist -s md_0_1.tpr -f md_0_1.xtc -o dist.xvg -n index.ndx
>>
>> Groups I selected was
>> Group 1 (protein)
>> Group 13 (ligand)
>>
>> It says the following error
>>
>> Molecule in topology has atom numbers below and above natoms (11793).
>> You are probably trying to use a trajectory which does not match the first
>> 11793 atoms of the run input file.
>>
>> how to debug the error...
>>
>> --
>>
>> Thanking You with Regards.
>>
>> Arunima Shilpi
>>
>> Ph. D Research Scholar(Cancer & Epigenetics)
>> Department of Life Science
>> National Institute of Technology
>> Rourkela
>> Odisha
>> --
>> gmx-users mailing list gmx-users at 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-request at gromacs.org.
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>
>
> ------------------------------
>
> Message: 5
> Date: Wed, 22 May 2013 07:09:36 -0700 (PDT)
> From: Andrish Reddy <areddy at csir.co.za>
> Subject: [gmx-users] C6 & C12 parameters for non-bonded interactions
> using tables
> To: gmx-users at gromacs.org
> Message-ID: <1369231776546-5008449.post at n6.nabble.com>
> Content-Type: text/plain; charset=us-ascii
>
> Greetings,
>
> I am trying to use tabulated potentials for the VdW interactions between
> TIP5P water molecules.
> I have tested my topology file to make sure that it gives reasonable results
> with the standard table6-12.xvg in the /top folder and C6=4*eps*sig^6 ,
> C12=4*eps*sig^12. I am able to match the energies with an identical run not
> using look-up tables. The problem comes when I want to include the C6 & C12
> parameters within the table. This is needed for dealing with more complex
> multi-parameter potential functions.
>
> I tried testing this with the standard Lennard-Jones potential. Setting
> g(r)=-(4*eps*sig^6)/r^6 and h(r)=(4*eps*sig^12)/r^12. I then construct my
> table according to [r,f(r),-f'(r),g(r),-g'(r),h(r),-h'(r)]
>
> I set vdw-type = user in my mdp file and modified my topology so that:
> [ defaults ]
> ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
> 1 1 yes 0.5 0.8333
>
> [ atomtypes ]
> ; name at.num mass charge ptype C6 C12
> OW_tip5p 8 16.00 0.0000 A 1.00000e+00 1.00000e+00
>
> Since C6 & C12 = 1, this run should be identical to using the table6-12.xvg
> and C6=4*eps*sig^6 , C12=4*eps*sig^12
> The run proceeds fine with no warnings or errors, but the LJ and Potential
> energies are an order of magnitude higher than when using the standard
> table. I don't understand why I am not able to reproduce the results by this
> method?
>
> Thanks,
> Andrish
>
>
>
>
> --
> View this message in context: http://gromacs.5086.x6.nabble.com/C6-C12-parameters-for-non-bonded-interactions-using-tables-tp5008449.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
>
>
> ------------------------------
>
> Message: 6
> Date: Wed, 22 May 2013 07:20:36 -0700 (PDT)
> From: Andrish Reddy <areddy at csir.co.za>
> Subject: [gmx-users] Re: error in running g_dist
> To: gmx-users at gromacs.org
> Message-ID: <1369232436002-5008450.post at n6.nabble.com>
> Content-Type: text/plain; charset=us-ascii
>
> Arunima Shilpi-2 wrote
>> Respected sir
>>
>> I want to calculate the distance between protein and ligand after I have
>> run the production step. I used the following command..
>>
>> g_dist -s md_0_1.tpr -f md_0_1.xtc -o dist.xvg -n index.ndx
>>
>> Groups I selected was
>> Group 1 (protein)
>> Group 13 (ligand)
>>
>> It says the following error
>>
>> Molecule in topology has atom numbers below and above natoms (11793).
>> You are probably trying to use a trajectory which does not match the first
>> 11793 atoms of the run input file.
>>
>> how to debug the error...
>>
>> --
>>
>> Thanking You with Regards.
>>
>> Arunima Shilpi
>>
>> Ph. D Research Scholar(Cancer & Epigenetics)
>> Department of Life Science
>> National Institute of Technology
>> Rourkela
>> Odisha
>> --
>> gmx-users mailing list
>
>> gmx-users@
>
>> 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-request@
>
>> .
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
> Did you check that this "You are probably trying to use a trajectory which
> does not match the first
> 11793 atoms of the run input file." is not the case?
>
> Andrish
>
>
>
> --
> View this message in context: http://gromacs.5086.x6.nabble.com/error-in-running-g-dist-tp5008444p5008450.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
>
>
> ------------------------------
>
> Message: 7
> Date: Wed, 22 May 2013 16:30:12 +0200
> From: Mark Abraham <mark.j.abraham at gmail.com>
> Subject: Re: [gmx-users] C6 & C12 parameters for non-bonded
> interactions using tables
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
> <CAMNuMARhWAvRgTgP1adfsxB11CfgS9D6qdTCEOda0x8vpkbgfA at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Exactly a factor of ten? Angstrom vs nm issue?
>
>
> On Wed, May 22, 2013 at 4:09 PM, Andrish Reddy <areddy at csir.co.za> wrote:
>
>> Greetings,
>>
>> I am trying to use tabulated potentials for the VdW interactions between
>> TIP5P water molecules.
>> I have tested my topology file to make sure that it gives reasonable
>> results
>> with the standard table6-12.xvg in the /top folder and C6=4*eps*sig^6 ,
>> C12=4*eps*sig^12. I am able to match the energies with an identical run
>> not
>> using look-up tables. The problem comes when I want to include the C6 & C12
>> parameters within the table. This is needed for dealing with more complex
>> multi-parameter potential functions.
>>
>> I tried testing this with the standard Lennard-Jones potential. Setting
>> g(r)=-(4*eps*sig^6)/r^6 and h(r)=(4*eps*sig^12)/r^12. I then construct my
>> table according to [r,f(r),-f'(r),g(r),-g'(r),h(r),-h'(r)]
>>
>> I set vdw-type = user in my mdp file and modified my topology so that:
>> [ defaults ]
>> ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
>> 1 1 yes 0.5 0.8333
>>
>> [ atomtypes ]
>> ; name at.num mass charge ptype C6 C12
>> OW_tip5p 8 16.00 0.0000 A 1.00000e+00 1.00000e+00
>>
>> Since C6 & C12 = 1, this run should be identical to using the table6-12.xvg
>> and C6=4*eps*sig^6 , C12=4*eps*sig^12
>> The run proceeds fine with no warnings or errors, but the LJ and Potential
>> energies are an order of magnitude higher than when using the standard
>> table. I don't understand why I am not able to reproduce the results by
>> this
>> method?
>>
>> Thanks,
>> Andrish
>>
>>
>>
>>
>> --
>> View this message in context:
>> http://gromacs.5086.x6.nabble.com/C6-C12-parameters-for-non-bonded-interactions-using-tables-tp5008449.html
>> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
>> --
>> gmx-users mailing list gmx-users at 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-request at gromacs.org.
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>
>
> ------------------------------
>
> Message: 8
> Date: Wed, 22 May 2013 14:30:20 +0000
> From: <L.Liu at utwente.nl>
> Subject: [gmx-users] COM coordinate fix
> To: <gmx-users at gromacs.org>
> Message-ID:
> <64B664D3F8234D4FA8C0BA7F66FEDBD03122CBA2 at EXMBX22.ad.utwente.nl>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear all,
>
> We have 80 polymers in the simulation box, for some reason, we want to make the COM of each polymer be fixed. Is this possible in Gromacs with any command, or somewhere in the source code we can change the expression of displacement along with time .
>
> Thank you very much in advance.
>
> Kind regards,
> Li
>
>
> ------------------------------
>
> --
> gmx-users mailing list
> gmx-users at 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 109, Issue 131
> *******************************************
>
More information about the gromacs.org_gmx-users
mailing list