[gmx-users] GROMACS mdp file for doing a single point energy after acpype conversion
Hi Justin
I obtained the following error with the following command and the mdp mentioned
below
gmx mdrun -s 1_OGNG_GLYCAM_SPE_GMX.tpr -rerun 1_OGNG_Amber.pdb
Thank you
Stéphane
--
Program: gmx mdrun, version 2018.1
Source file: src/programs/mdrun/runner.cpp (line 736)
Fatal error:
The .mdp file specified an energy mininization or normal mode algorithm, and
these are not compatible with mdrun -rerun
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
>> You also shouldn't use a minimizer when doing a zero-point energy. Use the
>> md integrator.
OK I try your suggestion
--
And the mdp
Message: 1
Date: Thu, 23 Apr 2020 06:18:33 -0400
From: Justin Lemkul
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] GROMACS mdp file for doing a single point
energy after acpype conversion
Message-ID: <28a2dc8e-20e9-abee-4b10-0f3cceb4f...@vt.edu>
Content-Type: text/plain; charset=utf-8; format=flowed
On 4/23/20 5:42 AM, ABEL Stephane wrote:
> Deal all,
>
> I am using acpype to convert a set of glycolipids modeled with the GLYCAM06
> force fiedl into the GROMACS format. acpype works well for this task. But I
> would like to check if the conversion is correctly done by performing single
> point energy (SPE) calculations with Amber and GROMACS codes and thus
> computes the energy differences for the bonded and non bonded terms
>
> For the former test I using the prmtop and inpcrd files generated with tleap
> and sander with the minimal commands below
>
> | mdin Single point
> &cntrl
> imin=0,
> maxcyc=0,
> ntmin=2,
> ntb=0,
> igb=0,
> cut=999
> /
>
> But For GROMACS vers > 5.0 and 2018.x , I did not find the equivalent mdp
> parameters that can be used for doing the same task. I I used the minimal
> file below The bonded energy terms are very similar between the two codes but
> not the non bonded terms
>
> integrator = steep ; Algorithm (steep = steepest descent
> minimization)
> emtol = 1000.0; Stop minimization when the maximum force <
> 1000.0 kJ/mol/nm
> emstep = 0.01 ; Minimization step size
> nsteps = 0 ; Maximum number of (minimization) steps to perform
> (should be 5)
>
> ; Parameters describing how to find the neighbors of each atom and how to
> calculate the interactions
> nstlist = 1 ; Frequency to update the neighbor list and long
> range forces
> cutoff-scheme = Group ; Buffered neighbor searching
> ns_type = grid ; Method to determine neighbor list (simple, grid)
> coulombtype = Cut-off ; Treatment of long range electrostatic
> interactions
> rcoulomb= 0 ; Short-range electrostatic cut-off
> rvdw= 0 ; Short-range Van der Waals cut-off
> rlist = 0
> pbc = no ; P
> continuation = yes
>
> I also also notice that a tpr generated with this mdp can not be used with
> -rerun argument so how I can compute a SPE equivalent to Sander
Why is it incompatible with mdrun -rerun? Do you get an error?
You also shouldn't use a minimizer when doing a zero-point energy. Use
the md integrator.
-Justin
--
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Re: [gmx-users] GROMACS mdp file for doing a single point energy after acpype conversion
On 4/23/20 5:42 AM, ABEL Stephane wrote: Deal all, I am using acpype to convert a set of glycolipids modeled with the GLYCAM06 force fiedl into the GROMACS format. acpype works well for this task. But I would like to check if the conversion is correctly done by performing single point energy (SPE) calculations with Amber and GROMACS codes and thus computes the energy differences for the bonded and non bonded terms For the former test I using the prmtop and inpcrd files generated with tleap and sander with the minimal commands below | mdin Single point &cntrl imin=0, maxcyc=0, ntmin=2, ntb=0, igb=0, cut=999 / But For GROMACS vers > 5.0 and 2018.x , I did not find the equivalent mdp parameters that can be used for doing the same task. I I used the minimal file below The bonded energy terms are very similar between the two codes but not the non bonded terms integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000.0; Stop minimization when the maximum force < 1000.0 kJ/mol/nm emstep = 0.01 ; Minimization step size nsteps = 0 ; Maximum number of (minimization) steps to perform (should be 5) ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces cutoff-scheme = Group ; Buffered neighbor searching ns_type = grid ; Method to determine neighbor list (simple, grid) coulombtype = Cut-off ; Treatment of long range electrostatic interactions rcoulomb= 0 ; Short-range electrostatic cut-off rvdw= 0 ; Short-range Van der Waals cut-off rlist = 0 pbc = no ; P continuation = yes I also also notice that a tpr generated with this mdp can not be used with -rerun argument so how I can compute a SPE equivalent to Sander Why is it incompatible with mdrun -rerun? Do you get an error? You also shouldn't use a minimizer when doing a zero-point energy. Use the md integrator. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] GROMACS mdp file for doing a single point energy after acpype conversion
Deal all, I am using acpype to convert a set of glycolipids modeled with the GLYCAM06 force fiedl into the GROMACS format. acpype works well for this task. But I would like to check if the conversion is correctly done by performing single point energy (SPE) calculations with Amber and GROMACS codes and thus computes the energy differences for the bonded and non bonded terms For the former test I using the prmtop and inpcrd files generated with tleap and sander with the minimal commands below | mdin Single point &cntrl imin=0, maxcyc=0, ntmin=2, ntb=0, igb=0, cut=999 / But For GROMACS vers > 5.0 and 2018.x , I did not find the equivalent mdp parameters that can be used for doing the same task. I I used the minimal file below The bonded energy terms are very similar between the two codes but not the non bonded terms integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000.0; Stop minimization when the maximum force < 1000.0 kJ/mol/nm emstep = 0.01 ; Minimization step size nsteps = 0 ; Maximum number of (minimization) steps to perform (should be 5) ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces cutoff-scheme = Group ; Buffered neighbor searching ns_type = grid ; Method to determine neighbor list (simple, grid) coulombtype = Cut-off ; Treatment of long range electrostatic interactions rcoulomb= 0 ; Short-range electrostatic cut-off rvdw= 0 ; Short-range Van der Waals cut-off rlist = 0 pbc = no ; P continuation = yes I also also notice that a tpr generated with this mdp can not be used with -rerun argument so how I can compute a SPE equivalent to Sander Thanks in advance for your help and suggestions Stéphane -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
