Re: [gmx-users] How to perform final MD simulation after extending a NPT simulation

[Mark Abraham]

Hi,

On Wed, Jun 21, 2017 at 3:24 AM Adarsh V. K. 
wrote:

> Dear all,
>
> *I used following command to extend a NPT simulation*
>
> 1) gmx convert-tpr -s npt.tpr -extend 500 -o tpxout.tpr
> gmx mdrun -deffnm tpxout -cpi npt.cpt -v
>
> but the analysis " gmx energy -f  *tpxout*.edr -o pressure.xvg " shows only
> the extended part; How to append the extend part to previous cpt


trjcat and eneconv


> and
> continue to production MD ?
>

You don't want to append all your equilibration data and then your
production data. You're going to discard your equilibration period before
you analyse the data you produce...

---
> *Now to do a final MD simulation what command I should use?*
>
> 2) gmx grompp -f md.mdp -c npt.gro -t *npt.cpt* -p topol.top -n index.ndx
> -o md_0_1.tpr
> gmx mdrun -deffnm md_0_1 -v
>
> or
>
> 3) gmx grompp -f md.mdp -c npt.gro -t *tpxout.cpt* -p topol.top -n
> index.ndx -o md_0_1.tpr
> gmx mdrun -deffnm md_0_1 -v
>

These are identical except for the grompp -t, which controls what
configuration is written to the .tpr. Choose the one that makes sense for
the point from which you are trying to start.

Mark

*no need to combine; just use the third command to continue to MD
> simulation?*
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[gmx-users] How to perform final MD simulation after extending a NPT simulation

[Adarsh V. K.]

Dear all,

*I used following command to extend a NPT simulation*

1) gmx convert-tpr -s npt.tpr -extend 500 -o tpxout.tpr
gmx mdrun -deffnm tpxout -cpi npt.cpt -v

but the analysis " gmx energy -f  *tpxout*.edr -o pressure.xvg " shows only
the extended part; How to append the extend part to previous cpt and
continue to production MD ?
---
*Now to do a final MD simulation what command I should use?*

2) gmx grompp -f md.mdp -c npt.gro -t *npt.cpt* -p topol.top -n index.ndx
-o md_0_1.tpr
gmx mdrun -deffnm md_0_1 -v

or

3) gmx grompp -f md.mdp -c npt.gro -t *tpxout.cpt* -p topol.top -n
index.ndx -o md_0_1.tpr
gmx mdrun -deffnm md_0_1 -v

*no need to combine; just use the third command to continue to MD
simulation?*
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Re: [gmx-users] How to perform final MD simulation after extending a NPT simulation

[Mark Abraham]

Hi

On Wed, May 31, 2017 at 2:50 AM Adarsh V. K. 
wrote:

> Dear all,
>
> *I used following command to extend a NPT simulation*
>
> gmx convert-tpr -s npt.tpr -extend 500 -o tpxout.tpr
> gmx mdrun -deffnm tpxout -cpi npt_prev.cpt -v
>

If the npt run was long enough, you'll have both npt.cpt and npt_prev.cpt
(as a backup). Use the one that was written later.


> *Now to do final MD simulation what command I should use?*
>
> gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o
> md_0_1.tpr
> gmx mdrun -deffnm md_0_1 -v
>
> or
>
> gmx grompp -f md.mdp -c npt.gro -t tpxout.cpt -p topol.top -n index.ndx -o
> md_0_1.tpr
> gmx mdrun -deffnm md_0_1 -v
>

Give to grompp -t the cpt file from the end of the run you're intending to
continue.

Using npt.cpt would be particularly strange if you used npt_prev.cpt to
extend the npt run and write tpxout, because now you've thrown away the
extended component.

Mark


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Re: [gmx-users] How to perform final MD simulation after extending a NPT simulation

[Justin Lemkul]

On 5/30/17 8:50 PM, Adarsh V. K. wrote:

Dear all,

*I used following command to extend a NPT simulation*

gmx convert-tpr -s npt.tpr -extend 500 -o tpxout.tpr
gmx mdrun -deffnm tpxout -cpi npt_prev.cpt -v

*Now to do final MD simulation what command I should use?*

gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o
md_0_1.tpr
gmx mdrun -deffnm md_0_1 -v

or

gmx grompp -f md.mdp -c npt.gro -t tpxout.cpt -p topol.top -n index.ndx -o
md_0_1.tpr
gmx mdrun -deffnm md_0_1 -v



I suggest you use gmx check to investigate the contents and differences between 
the checkpoint files.  If "npt" is the first part of the run, and "tpxout" is 
the second part, and you want to continue from the second part...


-Justin

--
==

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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] How to perform final MD simulation after extending a NPT simulation

[Adarsh V. K.]

Dear all,

*I used following command to extend a NPT simulation*

gmx convert-tpr -s npt.tpr -extend 500 -o tpxout.tpr
gmx mdrun -deffnm tpxout -cpi npt_prev.cpt -v

*Now to do final MD simulation what command I should use?*

gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o
md_0_1.tpr
gmx mdrun -deffnm md_0_1 -v

or

gmx grompp -f md.mdp -c npt.gro -t tpxout.cpt -p topol.top -n index.ndx -o
md_0_1.tpr
gmx mdrun -deffnm md_0_1 -v
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