Re: [gmx-users] I tried all the suggestions; but no improvement..! Fwd: Restart a stopped simulation after a power failure? : Not working in Gromacs 5.1.4

[Mark Abraham]

Hi,

On Fri, May 19, 2017 at 4:08 AM Adarsh V. K. 
wrote:

> Dear Dr. Mark and Justin,
>
> *I tried all the suggestions; but no improvement..! *
>
> gmx mdrun -deffnm md_0_1 -cpi md_0_1.cpt -v
>

I'm still guessing because you've never told us what your original mdrun
command was, but if your original command was

gmx mdrun -deffnm md_0_1 -v

and you've not modified any of those output files, then this does a restart
and appends to the output. mdrun will even tell you why it won't restart or
won't append, but you haven't shared the reason with us.

However, you've surely modified some of those original output files in your
attempts, so it can't work any more. Go and do your science, now that you
know what the procedure for a restart is. :-)

*also tried*
>
> gmx mdrun -deffnm md_0_1.tpr -cpi md_0_1_prev.cpt -v
>
>
> *gives errors asking for an ' s ' flag...!*
>

Yes, there's a reason we didn't tell you to try that.


> -
>
> *The below command works and it starts a log file ,md.log,  but no
> appending  md_0_1.log (Please see the attached files and details).*
>
> gmx mdrun -s md_0_1.tpr -cpi md_0_1_prev.cpt -v
>

This cannot append to md_0_1.log because you've told mdrun the log file is
named (the default) md.log.

Mark
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Re: [gmx-users] Using CHARMM36 in GROMACS to simulate polysaccharides

[Mohammad Hassan Khatami]

Thanks Justin. 
I have tried the CHARMM-GUI but it crashed. I might need to modify the order of 
the atoms in my PDB file, which I have created using GLYCAM-Web GUI. I have 
downloaded the “toppar_c36_feb16” but I did not find a manual on how to apply 
them (any suggestions?), so it did not go far.
I'll play with these two, and I'll be back.
MH
> On May 18, 2017, at 5:08 PM, Justin Lemkul  wrote:
> 
> 
> 
> On 5/18/17 4:57 PM, Mohammad Hassan Khatami wrote:
>> Hi,
>> 
>> I am trying to run simulations on alpha-D-glucose polymers. I have done 
>> these simulations using AMBER and I am wondering if it is possible to run 
>> them employing CHARMM36 in GROMACS, as well?
>> It seams that CHARMM36 in GROMACS has only implemented monomers of 
>> alpha-D-glucose as ”AGLC”. Is there a way to introduce the whole polymer to 
>> the GROMACS?
>> 
> 
> Sure, you can treat it like any polymer, but you'll have to create the 
> internal monomer residues yourself from the patches in the original CHARMM 
> force field files.
> 
> Or try CHARMM-GUI; it should handle what you need and give you all the 
> necessary GROMACS inputs.
> 
> -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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Re: [gmx-users] Using CHARMM36 in GROMACS to simulate polysaccharides

[Justin Lemkul]

On 5/18/17 4:57 PM, Mohammad Hassan Khatami wrote:

Hi,

I am trying to run simulations on alpha-D-glucose polymers. I have done these 
simulations using AMBER and I am wondering if it is possible to run them 
employing CHARMM36 in GROMACS, as well?
It seams that CHARMM36 in GROMACS has only implemented monomers of 
alpha-D-glucose as ”AGLC”. Is there a way to introduce the whole polymer to the 
GROMACS?



Sure, you can treat it like any polymer, but you'll have to create the internal 
monomer residues yourself from the patches in the original CHARMM force field files.


Or try CHARMM-GUI; it should handle what you need and give you all the necessary 
GROMACS inputs.


-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] Using CHARMM36 in GROMACS to simulate polysaccharides

[Mohammad Hassan Khatami]

Hi,

I am trying to run simulations on alpha-D-glucose polymers. I have done these 
simulations using AMBER and I am wondering if it is possible to run them 
employing CHARMM36 in GROMACS, as well? 
It seams that CHARMM36 in GROMACS has only implemented monomers of 
alpha-D-glucose as ”AGLC”. Is there a way to introduce the whole polymer to the 
GROMACS?

Best,
Mohammad
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Re: [gmx-users] Error message

[Mark Abraham]

Hi,

We can't tell anything from your description of your method. Obviously you
have to declare your atomtypes before you use them, so either it's not
declared, or you think it's declared but haven't organized the files
properly (e.g. included the wrong one).

Mark

On Thu, May 18, 2017 at 7:33 PM Pandya, Akash 
wrote:

> Hi,
>
> Thank you for your response. A new issue has arisen. The itp file was
> generated from SWISS PARAM. I don't understand why it can't recognise the
> NRP atomtype for Nitrogen.
>
> ERROR 1 [file GLY.itp, line 17]:
>   Atomtype NRP not found
>
> Akash
> -Original Message-
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark
> Abraham
> Sent: 18 May 2017 18:03
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Error message
>
> Hi,
>
> A molecule itp does not stand in isolation.
>
> From that link "If the directive in question is atomtypes (which is the
> most common source of this error) or any other bonded or nonbonded [*types]
> directive, typically the user is adding some non-standard species (ligand,
> solvent, etc) that introduces new atom types or parameters into the system.
> As indicated above, these new types and parameters must appear before any
> [moleculetype] directive. The force field has to be fully constructed
> before any molecules can be defined."
>
> Probably you're including that .itp after some other [moleculetype].
> Declare all the atom types before any moleculetypes, like chapter 5 of the
> reference manual documents.
>
> Mark
>
> On Thu, May 18, 2017 at 6:47 PM Pandya, Akash 
> wrote:
>
> > Sorry for replying on the wrong thread. I've read the errors
> > documentation. The atomtypes directive does appear before any molecule
> > types directive in my itp file. I tried changing the order it still
> > comes up as an error
> >
> > [ atomtypes ]
> > ; name atomnum  masscharge  ptype sigma epsilon
> > CR 6   12.0110   0.0A  0.3875410.230120
> > CO2M   6   12.0110   0.0A  0.3563590.292880
> > HCMM   11.0079   0.0A  0.2351970.092048
> > HNRP   11.0079   0.0A  0.0400010.192464
> > NRP7   14.0067   0.0A  0.3296320.836800
> > O2CM   8   15.9994   0.0A  0.3029050.502080
> >
> > -Original Message-
> > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
> > gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin
> > Lemkul
> > Sent: 18 May 2017 17:00
> > To: gmx-us...@gromacs.org
> > Subject: Re: [gmx-users] Error message
> >
> >
> >
> > On 5/18/17 11:57 AM, Pandya, Akash wrote:
> > > Hi all,
> > >
> > > I've been trying to figure out the error message below but I'm not
> > getting anywhere. I have attached my relevant itp file. Please could
> > someone tell me what is wrong with my itp file?
> > >
> >
> > Googling the error usually turns something up...
> >
> > http://www.gromacs.org/Documentation/Errors#Invalid_order_for_directiv
> > e_xxx
> >
> > For future reference, the list does not accept attachments.
> >
> > -Justin
> >
> > >
> > > Fatal error:
> > > Syntax error - File GLY.itp, line 7
> > > Last line read:
> > > '[ atomtypes ] '
> > > Invalid order for directive atomtypes
> > >
> > >
> > > Best regards,
> > >
> > > Akash
> > >
> > >
> > >
> >
> > --
> > ==
> >
> > 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
> >
> > ==
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
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> >
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> > send a mail to gmx-users-requ...@gromacs.org.
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Re: [gmx-users] Error message

[Pandya, Akash]

Hi,

Thank you for your response. A new issue has arisen. The itp file was generated 
from SWISS PARAM. I don't understand why it can't recognise the NRP atomtype 
for Nitrogen.

ERROR 1 [file GLY.itp, line 17]:
  Atomtype NRP not found

Akash
-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark 
Abraham
Sent: 18 May 2017 18:03
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Error message

Hi,

A molecule itp does not stand in isolation.

>From that link "If the directive in question is atomtypes (which is the most 
>common source of this error) or any other bonded or nonbonded [*types] 
>directive, typically the user is adding some non-standard species (ligand, 
>solvent, etc) that introduces new atom types or parameters into the system.
As indicated above, these new types and parameters must appear before any 
[moleculetype] directive. The force field has to be fully constructed before 
any molecules can be defined."

Probably you're including that .itp after some other [moleculetype].
Declare all the atom types before any moleculetypes, like chapter 5 of the 
reference manual documents.

Mark

On Thu, May 18, 2017 at 6:47 PM Pandya, Akash 
wrote:

> Sorry for replying on the wrong thread. I've read the errors 
> documentation. The atomtypes directive does appear before any molecule 
> types directive in my itp file. I tried changing the order it still 
> comes up as an error
>
> [ atomtypes ]
> ; name atomnum  masscharge  ptype sigma epsilon
> CR 6   12.0110   0.0A  0.3875410.230120
> CO2M   6   12.0110   0.0A  0.3563590.292880
> HCMM   11.0079   0.0A  0.2351970.092048
> HNRP   11.0079   0.0A  0.0400010.192464
> NRP7   14.0067   0.0A  0.3296320.836800
> O2CM   8   15.9994   0.0A  0.3029050.502080
>
> -Original Message-
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin 
> Lemkul
> Sent: 18 May 2017 17:00
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Error message
>
>
>
> On 5/18/17 11:57 AM, Pandya, Akash wrote:
> > Hi all,
> >
> > I've been trying to figure out the error message below but I'm not
> getting anywhere. I have attached my relevant itp file. Please could 
> someone tell me what is wrong with my itp file?
> >
>
> Googling the error usually turns something up...
>
> http://www.gromacs.org/Documentation/Errors#Invalid_order_for_directiv
> e_xxx
>
> For future reference, the list does not accept attachments.
>
> -Justin
>
> >
> > Fatal error:
> > Syntax error - File GLY.itp, line 7
> > Last line read:
> > '[ atomtypes ] '
> > Invalid order for directive atomtypes
> >
> >
> > Best regards,
> >
> > Akash
> >
> >
> >
>
> --
> ==
>
> 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
>
> ==
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before 
> posting!
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Re: [gmx-users] Error message

[Mark Abraham]

Hi,

A molecule itp does not stand in isolation.

>From that link "If the directive in question is atomtypes (which is the
most common source of this error) or any other bonded or nonbonded [*types]
directive, typically the user is adding some non-standard species (ligand,
solvent, etc) that introduces new atom types or parameters into the system.
As indicated above, these new types and parameters must appear before any
[moleculetype] directive. The force field has to be fully constructed
before any molecules can be defined."

Probably you're including that .itp after some other [moleculetype].
Declare all the atom types before any moleculetypes, like chapter 5 of the
reference manual documents.

Mark

On Thu, May 18, 2017 at 6:47 PM Pandya, Akash 
wrote:

> Sorry for replying on the wrong thread. I've read the errors
> documentation. The atomtypes directive does appear before any molecule
> types directive in my itp file. I tried changing the order it still comes
> up as an error
>
> [ atomtypes ]
> ; name atomnum  masscharge  ptype sigma epsilon
> CR 6   12.0110   0.0A  0.3875410.230120
> CO2M   6   12.0110   0.0A  0.3563590.292880
> HCMM   11.0079   0.0A  0.2351970.092048
> HNRP   11.0079   0.0A  0.0400010.192464
> NRP7   14.0067   0.0A  0.3296320.836800
> O2CM   8   15.9994   0.0A  0.3029050.502080
>
> -Original Message-
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin
> Lemkul
> Sent: 18 May 2017 17:00
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Error message
>
>
>
> On 5/18/17 11:57 AM, Pandya, Akash wrote:
> > Hi all,
> >
> > I've been trying to figure out the error message below but I'm not
> getting anywhere. I have attached my relevant itp file. Please could
> someone tell me what is wrong with my itp file?
> >
>
> Googling the error usually turns something up...
>
> http://www.gromacs.org/Documentation/Errors#Invalid_order_for_directive_xxx
>
> For future reference, the list does not accept attachments.
>
> -Justin
>
> >
> > Fatal error:
> > Syntax error - File GLY.itp, line 7
> > Last line read:
> > '[ atomtypes ] '
> > Invalid order for directive atomtypes
> >
> >
> > Best regards,
> >
> > Akash
> >
> >
> >
>
> --
> ==
>
> 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
>
> ==
> --
> 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
>
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Re: [gmx-users] Error message

[Pandya, Akash]

Sorry for replying on the wrong thread. I've read the errors documentation. The 
atomtypes directive does appear before any molecule types directive in my itp 
file. I tried changing the order it still comes up as an error

[ atomtypes ]
; name atomnum  masscharge  ptype sigma epsilon
CR 6   12.0110   0.0A  0.3875410.230120
CO2M   6   12.0110   0.0A  0.3563590.292880
HCMM   11.0079   0.0A  0.2351970.092048
HNRP   11.0079   0.0A  0.0400010.192464
NRP7   14.0067   0.0A  0.3296320.836800
O2CM   8   15.9994   0.0A  0.3029050.502080

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin 
Lemkul
Sent: 18 May 2017 17:00
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Error message



On 5/18/17 11:57 AM, Pandya, Akash wrote:
> Hi all,
>
> I've been trying to figure out the error message below but I'm not getting 
> anywhere. I have attached my relevant itp file. Please could someone tell me 
> what is wrong with my itp file?
>

Googling the error usually turns something up...

http://www.gromacs.org/Documentation/Errors#Invalid_order_for_directive_xxx

For future reference, the list does not accept attachments.

-Justin

>
> Fatal error:
> Syntax error - File GLY.itp, line 7
> Last line read:
> '[ atomtypes ] '
> Invalid order for directive atomtypes
>
>
> Best regards,
>
> Akash
>
>
>

--
==

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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Re: [gmx-users] Can you please tell me the exact command? Re: Restart a stopped simulation after a power failure? : Not working in Gromacs 5.1.4

[Justin Lemkul]

On 5/18/17 12:44 PM, Pandya, Akash wrote:

I've read the errors documentation. The atomtypes directive does appear before 
any molecule types directive in my itp file. I tried changing the order it 
still comes up as an error



Table 5.4 in the PDF manual has the order that directives must appear.  Your 
[atomtypes] must be out of order with respect to some other directive.


-Justin


[ atomtypes ]
; name atomnum  masscharge  ptype sigma epsilon
CR 6   12.0110   0.0A  0.3875410.230120
CO2M   6   12.0110   0.0A  0.3563590.292880
HCMM   11.0079   0.0A  0.2351970.092048
HNRP   11.0079   0.0A  0.0400010.192464
NRP7   14.0067   0.0A  0.3296320.836800
O2CM   8   15.9994   0.0A  0.3029050.502080

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin 
Lemkul
Sent: 18 May 2017 16:33
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Can you please tell me the exact command? Re: Restart 
a stopped simulation after a power failure? : Not working in Gromacs 5.1.4



On 5/18/17 11:30 AM, Adarsh V. K. wrote:

Dear Dr. Mark,

Thank you for the prompt reply. I have been struggling with the issue
for couple month time. Would you please advise me how to use  "
-deffnm " flag in commands?

# gmx mdrun  -s  md_0_1.tpr  -cpi  md_0_1_prev.cpt  -v  -deffnm

Will the above command will successful restart a stopped simulation
and append?, If no could you please type the exact command I
should use to solve the issue.



The -deffnm command sets the default file prefix for all output files.  So if 
you issue:

gmx mdrun -deffnm md_0_1

You will get all files name md_0_1.* as output.

If you extend the simulation (e.g. gmx convert-tpr -extend) and keep the same 
file name (e.g. md_0_1.tpr now just contains more steps)

gmx mdrun -deffnm md_0_1 -cpi md_0_1.cpt

That's all there is to it.

-Justin


Sincerely,

Adarsh V. K.
Research Scholar (PhD)
National Institute of Technology, Calicut ( NIT C ) Kerala state,
India

--
 On Thu, May 18, 2017 at 7:13 PM, Mark Abraham

wrote:


Hi,

Some of your commands and outputs are inconsistent. You can't get
md_0_1.log without e.g. using -deffnm, and you'll only get md.log if
you don't use deffnm. But if you change that when trying to do your
continuation, mdrun won't know how to append because you haven't told
it that the old name. Be consistent. Your whole trajectory is present
in all your output files, but you're going to have to concatenate
them yourself, e.g. with gmx trjcat since you didn't tell mdrun a
consistent name for the files.

GROMACS 2016 likely refuses to do your continuation, precisely so
that you are prompted to say what you actually want, rather than
mdrun trying to be clever and getting it wrong.

Mark

On Thu, May 18, 2017 at 11:03 AM Adarsh V. K.

wrote:


Dear gmx users,

I use Gromacs 5.1.4 for protein ligand simulation. How can I restart
a stopped simulation after a power failure? (used 8 processor cores
+ Graphics card GTX 780Ti).

I have attached the log file along with this mail.

It appeared that no details appended after restarting simulation
(after power failure at 3.5 ns), Even Though the 'terminal' Ubuntu
16.04 shows that the simulation successfully restarted from 3.5 ns
(used 8 processor cores + Graphics card GTX 780Ti) and completed the
entire 8 ns simulation...!!. Frames...350 -> 3500 ps (not appended
the log file after the restart from 3500ps to 8000ps).

I used the command (gromacs 5.1.4),
  # gmx mdrun -s md_0_1.tpr -cpi md_0_1_prev.cpt -v

I also tried, # gmx mdrun -s md_0_1.tpr -cpi md_0_1_prev.cpt -append



md_0_1.log : (final)
-
Step   Time Lambda
1765000 3530.00.0

   Energies (kJ/mol)
   G96AngleProper Dih.  Improper Dih.  LJ-14
Coulomb-14
6.73096e+033.13198e+032.15931e+031.31375e+03
4.51549e+04
LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
Potential
3.66659e+05   -7.80170e+03   -2.71529e+064.12416e+03
-2.29382e+06
Kinetic En.   Total EnergyTemperature Pres. DC (bar) Pressure
(bar)
4.12474e+05   -1.88135e+063.00209e+02   -7.62778e+01
2.10104e+01
   Constr. rmsd
2.37431e-05

-
md.log (final)
--
Step   Time Lambda
400 8000.00.0

Writing checkpoint, step 400 at Thu May 18 13:55:01 2017


   Energies (kJ/mol)
   G96AngleProper Dih.  Improper Dih.  

Re: [gmx-users] Can you please tell me the exact command? Re: Restart a stopped simulation after a power failure? : Not working in Gromacs 5.1.4

[Pandya, Akash]

I've read the errors documentation. The atomtypes directive does appear before 
any molecule types directive in my itp file. I tried changing the order it 
still comes up as an error

[ atomtypes ] 
; name atomnum  masscharge  ptype sigma epsilon 
CR 6   12.0110   0.0A  0.3875410.230120  
CO2M   6   12.0110   0.0A  0.3563590.292880   
HCMM   11.0079   0.0A  0.2351970.092048  
HNRP   11.0079   0.0A  0.0400010.192464  
NRP7   14.0067   0.0A  0.3296320.836800  
O2CM   8   15.9994   0.0A  0.3029050.502080

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin 
Lemkul
Sent: 18 May 2017 16:33
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Can you please tell me the exact command? Re: Restart 
a stopped simulation after a power failure? : Not working in Gromacs 5.1.4



On 5/18/17 11:30 AM, Adarsh V. K. wrote:
> Dear Dr. Mark,
>
> Thank you for the prompt reply. I have been struggling with the issue 
> for couple month time. Would you please advise me how to use  " 
> -deffnm " flag in commands?
>
> # gmx mdrun  -s  md_0_1.tpr  -cpi  md_0_1_prev.cpt  -v  -deffnm
>
> Will the above command will successful restart a stopped simulation 
> and append?, If no could you please type the exact command I 
> should use to solve the issue.
>

The -deffnm command sets the default file prefix for all output files.  So if 
you issue:

gmx mdrun -deffnm md_0_1

You will get all files name md_0_1.* as output.

If you extend the simulation (e.g. gmx convert-tpr -extend) and keep the same 
file name (e.g. md_0_1.tpr now just contains more steps)

gmx mdrun -deffnm md_0_1 -cpi md_0_1.cpt

That's all there is to it.

-Justin

> Sincerely,
>
> Adarsh V. K.
> Research Scholar (PhD)
> National Institute of Technology, Calicut ( NIT C ) Kerala state, 
> India
>
> --
>  On Thu, May 18, 2017 at 7:13 PM, Mark Abraham 
> 
> wrote:
>
>> Hi,
>>
>> Some of your commands and outputs are inconsistent. You can't get 
>> md_0_1.log without e.g. using -deffnm, and you'll only get md.log if 
>> you don't use deffnm. But if you change that when trying to do your 
>> continuation, mdrun won't know how to append because you haven't told 
>> it that the old name. Be consistent. Your whole trajectory is present 
>> in all your output files, but you're going to have to concatenate 
>> them yourself, e.g. with gmx trjcat since you didn't tell mdrun a 
>> consistent name for the files.
>>
>> GROMACS 2016 likely refuses to do your continuation, precisely so 
>> that you are prompted to say what you actually want, rather than 
>> mdrun trying to be clever and getting it wrong.
>>
>> Mark
>>
>> On Thu, May 18, 2017 at 11:03 AM Adarsh V. K. 
>> 
>> wrote:
>>
>>> Dear gmx users,
>>>
>>> I use Gromacs 5.1.4 for protein ligand simulation. How can I restart 
>>> a stopped simulation after a power failure? (used 8 processor cores 
>>> + Graphics card GTX 780Ti).
>>>
>>> I have attached the log file along with this mail.
>>>
>>> It appeared that no details appended after restarting simulation 
>>> (after power failure at 3.5 ns), Even Though the 'terminal' Ubuntu 
>>> 16.04 shows that the simulation successfully restarted from 3.5 ns 
>>> (used 8 processor cores + Graphics card GTX 780Ti) and completed the 
>>> entire 8 ns simulation...!!. Frames...350 -> 3500 ps (not appended 
>>> the log file after the restart from 3500ps to 8000ps).
>>>
>>> I used the command (gromacs 5.1.4),
>>>   # gmx mdrun -s md_0_1.tpr -cpi md_0_1_prev.cpt -v
>>>
>>> I also tried, # gmx mdrun -s md_0_1.tpr -cpi md_0_1_prev.cpt -append
>>>
>>> 
>>> 
>>> md_0_1.log : (final)
>>> -
>>> Step   Time Lambda
>>> 1765000 3530.00.0
>>>
>>>Energies (kJ/mol)
>>>G96AngleProper Dih.  Improper Dih.  LJ-14
>>> Coulomb-14
>>> 6.73096e+033.13198e+032.15931e+031.31375e+03
>>> 4.51549e+04
>>> LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>>> Potential
>>> 3.66659e+05   -7.80170e+03   -2.71529e+064.12416e+03
>>> -2.29382e+06
>>> Kinetic En.   Total EnergyTemperature Pres. DC (bar) Pressure
>>> (bar)
>>> 4.12474e+05   -1.88135e+063.00209e+02   -7.62778e+01
>>> 2.10104e+01
>>>Constr. rmsd
>>> 2.37431e-05
>>> 
>>> -
>>> md.log (final)
>>> --
>>> Step   Time Lambda
>>> 400 8000.00.0
>>>
>>> Writing checkpoint, step 

Re: [gmx-users] Can you please tell me the exact command? Re: Restart a stopped simulation after a power failure? : Not working in Gromacs 5.1.4

[Justin Lemkul]

On 5/18/17 11:30 AM, Adarsh V. K. wrote:

Dear Dr. Mark,

Thank you for the prompt reply. I have been struggling with the issue for
couple month time. Would you please advise me how to use  " -deffnm " flag
in commands?

# gmx mdrun  -s  md_0_1.tpr  -cpi  md_0_1_prev.cpt  -v  -deffnm

Will the above command will successful restart a stopped simulation and
append?, If no could you please type the exact command I should use to
solve the issue.



The -deffnm command sets the default file prefix for all output files.  So if 
you issue:


gmx mdrun -deffnm md_0_1

You will get all files name md_0_1.* as output.

If you extend the simulation (e.g. gmx convert-tpr -extend) and keep the same 
file name (e.g. md_0_1.tpr now just contains more steps)


gmx mdrun -deffnm md_0_1 -cpi md_0_1.cpt

That's all there is to it.

-Justin


Sincerely,

Adarsh V. K.
Research Scholar (PhD)
National Institute of Technology, Calicut ( NIT C )
Kerala state, India

--
On Thu, May 18, 2017 at 7:13 PM, Mark Abraham 
wrote:


Hi,

Some of your commands and outputs are inconsistent. You can't get
md_0_1.log without e.g. using -deffnm, and you'll only get md.log if you
don't use deffnm. But if you change that when trying to do your
continuation, mdrun won't know how to append because you haven't told it
that the old name. Be consistent. Your whole trajectory is present in all
your output files, but you're going to have to concatenate them yourself,
e.g. with gmx trjcat since you didn't tell mdrun a consistent name for the
files.

GROMACS 2016 likely refuses to do your continuation, precisely so that you
are prompted to say what you actually want, rather than mdrun trying to be
clever and getting it wrong.

Mark

On Thu, May 18, 2017 at 11:03 AM Adarsh V. K. 
wrote:


Dear gmx users,

I use Gromacs 5.1.4 for protein ligand simulation. How can I restart a
stopped simulation after a power failure? (used 8 processor cores +
Graphics card GTX 780Ti).

I have attached the log file along with this mail.

It appeared that no details appended after restarting simulation (after
power failure at 3.5 ns), Even Though the 'terminal' Ubuntu 16.04 shows
that the simulation successfully restarted from 3.5 ns (used 8 processor
cores + Graphics card GTX 780Ti) and completed the entire 8 ns
simulation...!!. Frames...350 -> 3500 ps (not appended the log file after
the restart from 3500ps to 8000ps).

I used the command (gromacs 5.1.4),
  # gmx mdrun -s md_0_1.tpr -cpi md_0_1_prev.cpt -v

I also tried, # gmx mdrun -s md_0_1.tpr -cpi md_0_1_prev.cpt -append



md_0_1.log : (final)
-
Step   Time Lambda
1765000 3530.00.0

   Energies (kJ/mol)
   G96AngleProper Dih.  Improper Dih.  LJ-14
Coulomb-14
6.73096e+033.13198e+032.15931e+031.31375e+03
4.51549e+04
LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
Potential
3.66659e+05   -7.80170e+03   -2.71529e+064.12416e+03
-2.29382e+06
Kinetic En.   Total EnergyTemperature Pres. DC (bar) Pressure
(bar)
4.12474e+05   -1.88135e+063.00209e+02   -7.62778e+01
2.10104e+01
   Constr. rmsd
2.37431e-05

-
md.log (final)
--
Step   Time Lambda
400 8000.00.0

Writing checkpoint, step 400 at Thu May 18 13:55:01 2017


   Energies (kJ/mol)
   G96AngleProper Dih.  Improper Dih.  LJ-14
Coulomb-14
6.44959e+033.18212e+032.06343e+031.53953e+03
4.49878e+04
LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
Potential
3.66131e+05   -7.78489e+03   -2.71259e+064.78708e+03
-2.29124e+06
Kinetic En.   Total EnergyTemperature Pres. DC (bar) Pressure
(bar)
4.13852e+05   -1.87738e+063.01212e+02   -7.59495e+01
5.34060e+01
   Constr. rmsd
2.33151e-05
-
Force evaluation time GPU/CPU: 12.005 ms/12.263 ms = 0.979
For optimal performance this ratio should be close to 1!

   Core t (s)   Wall t (s)(%)
   Time:   312346.79739374.380  793.3
 10h56:14
 (ns/day)(hour/ns)
Performance:9.9672.408
Finished mdrun on rank 0 Thu May 18 13:55:02 2017


---
But while using the command it shows only 3.5 ns of simulation. How to
solve this problem

gmx trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_0_1_noPBC.xtc -pbc mol -ur
compact

Select 0 ("System")

-

Later I repeated the whole 8 ns 

Re: [gmx-users] Error message

[Justin Lemkul]

On 5/18/17 11:57 AM, Pandya, Akash wrote:

Hi all,

I've been trying to figure out the error message below but I'm not getting 
anywhere. I have attached my relevant itp file. Please could someone tell me 
what is wrong with my itp file?



Googling the error usually turns something up...

http://www.gromacs.org/Documentation/Errors#Invalid_order_for_directive_xxx

For future reference, the list does not accept attachments.

-Justin



Fatal error:
Syntax error - File GLY.itp, line 7
Last line read:
'[ atomtypes ] '
Invalid order for directive atomtypes


Best regards,

Akash





--
==

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

==
--
Gromacs Users mailing list

* Please search the archive at 
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* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
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mail to gmx-users-requ...@gromacs.org.

[gmx-users] Error message

[Pandya, Akash]

Hi all,

I've been trying to figure out the error message below but I'm not getting 
anywhere. I have attached my relevant itp file. Please could someone tell me 
what is wrong with my itp file?


Fatal error:
Syntax error - File GLY.itp, line 7
Last line read:
'[ atomtypes ] '
Invalid order for directive atomtypes


Best regards,

Akash
-- 
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.

Re: [gmx-users] Can you please tell me the exact command? Re: Restart a stopped simulation after a power failure? : Not working in Gromacs 5.1.4

[Anshul Lahariya]

Hlw

Plzz use

gmx mdrun -v -deffnm md_0_1 -cpi md_0_1.cpt

On 18 May 2017 9:01 p.m., "Adarsh V. K." 
wrote:

> Dear Dr. Mark,
>
> Thank you for the prompt reply. I have been struggling with the issue for
> couple month time. Would you please advise me how to use  " -deffnm " flag
> in commands?
>
> # gmx mdrun  -s  md_0_1.tpr  -cpi  md_0_1_prev.cpt  -v  -deffnm
>
> Will the above command will successful restart a stopped simulation and
> append?, If no could you please type the exact command I should use to
> solve the issue.
>
> Sincerely,
>
> Adarsh V. K.
> Research Scholar (PhD)
> National Institute of Technology, Calicut ( NIT C )
> Kerala state, India
>
> --
> On Thu, May 18, 2017 at 7:13 PM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > Some of your commands and outputs are inconsistent. You can't get
> > md_0_1.log without e.g. using -deffnm, and you'll only get md.log if you
> > don't use deffnm. But if you change that when trying to do your
> > continuation, mdrun won't know how to append because you haven't told it
> > that the old name. Be consistent. Your whole trajectory is present in all
> > your output files, but you're going to have to concatenate them yourself,
> > e.g. with gmx trjcat since you didn't tell mdrun a consistent name for
> the
> > files.
> >
> > GROMACS 2016 likely refuses to do your continuation, precisely so that
> you
> > are prompted to say what you actually want, rather than mdrun trying to
> be
> > clever and getting it wrong.
> >
> > Mark
> >
> > On Thu, May 18, 2017 at 11:03 AM Adarsh V. K. <
> adarsh_p13008...@nitc.ac.in>
> > wrote:
> >
> >> Dear gmx users,
> >>
> >> I use Gromacs 5.1.4 for protein ligand simulation. How can I restart a
> >> stopped simulation after a power failure? (used 8 processor cores +
> >> Graphics card GTX 780Ti).
> >>
> >> I have attached the log file along with this mail.
> >>
> >> It appeared that no details appended after restarting simulation (after
> >> power failure at 3.5 ns), Even Though the 'terminal' Ubuntu 16.04 shows
> >> that the simulation successfully restarted from 3.5 ns (used 8 processor
> >> cores + Graphics card GTX 780Ti) and completed the entire 8 ns
> >> simulation...!!. Frames...350 -> 3500 ps (not appended the log file
> after
> >> the restart from 3500ps to 8000ps).
> >>
> >> I used the command (gromacs 5.1.4),
> >>   # gmx mdrun -s md_0_1.tpr -cpi md_0_1_prev.cpt -v
> >>
> >> I also tried, # gmx mdrun -s md_0_1.tpr -cpi md_0_1_prev.cpt -append
> >>
> >> 
> >> 
> >> md_0_1.log : (final)
> >> -
> >> Step   Time Lambda
> >> 1765000 3530.00.0
> >>
> >>Energies (kJ/mol)
> >>G96AngleProper Dih.  Improper Dih.  LJ-14
> >> Coulomb-14
> >> 6.73096e+033.13198e+032.15931e+031.31375e+03
> >> 4.51549e+04
> >> LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
> >> Potential
> >> 3.66659e+05   -7.80170e+03   -2.71529e+064.12416e+03
> >> -2.29382e+06
> >> Kinetic En.   Total EnergyTemperature Pres. DC (bar) Pressure
> >> (bar)
> >> 4.12474e+05   -1.88135e+063.00209e+02   -7.62778e+01
> >> 2.10104e+01
> >>Constr. rmsd
> >> 2.37431e-05
> >> 
> >> -
> >> md.log (final)
> >> --
> >> Step   Time Lambda
> >> 400 8000.00.0
> >>
> >> Writing checkpoint, step 400 at Thu May 18 13:55:01 2017
> >>
> >>
> >>Energies (kJ/mol)
> >>G96AngleProper Dih.  Improper Dih.  LJ-14
> >> Coulomb-14
> >> 6.44959e+033.18212e+032.06343e+031.53953e+03
> >> 4.49878e+04
> >> LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
> >> Potential
> >> 3.66131e+05   -7.78489e+03   -2.71259e+064.78708e+03
> >> -2.29124e+06
> >> Kinetic En.   Total EnergyTemperature Pres. DC (bar) Pressure
> >> (bar)
> >> 4.13852e+05   -1.87738e+063.01212e+02   -7.59495e+01
> >> 5.34060e+01
> >>Constr. rmsd
> >> 2.33151e-05
> >> -
> >> Force evaluation time GPU/CPU: 12.005 ms/12.263 ms = 0.979
> >> For optimal performance this ratio should be close to 1!
> >>
> >>Core t (s)   Wall t (s)(%)
> >>Time:   312346.79739374.380  793.3
> >>  10h56:14
> >>  (ns/day)(hour/ns)
> >> Performance:9.9672.408
> >> Finished mdrun on rank 0 Thu May 18 13:55:02 2017
> >>
> >> 
> >> ---
> >> But while using the command it shows only 3.5 ns of simulation. How to
> >> solve this problem
> >>
> >> 

Re: [gmx-users] Can you please tell me the exact command? Re: Restart a stopped simulation after a power failure? : Not working in Gromacs 5.1.4

[Mark Abraham]

Hi,

Use

gmx mdrun
gmx mdrun -cpi

so that by default you get appending and the filenames haven't changed.
Later, when you're comfortable, try

gmx mdrun -deffnm whatever
gmx mdrun -deffnm whatever -cpi

but really there's very few cases where deffnm is actually useful. You have
a directory name for organizing your work - do only one simulation in it
and avoid problems from trying to name each file descriptively.

Your problems likely stem from trying to do

gmx mdrun -deffnm whatever
gmx mdrun -s whatever -cpi

but it's hard to guess what you've done from partial reports. If so, you
can do it better by doing

gmx mdrun -deffnm whatever -cpi

Now, you probably need to do

gmx trjcat -f whatever traj -o combined

to get all your output into one file

Hope this helps!

Mark

On Thu, May 18, 2017 at 5:31 PM Adarsh V. K. 
wrote:

> Dear Dr. Mark,
>
> Thank you for the prompt reply. I have been struggling with the issue for
> couple month time. Would you please advise me how to use  " -deffnm " flag
> in commands?
>
> # gmx mdrun  -s  md_0_1.tpr  -cpi  md_0_1_prev.cpt  -v  -deffnm
>
> Will the above command will successful restart a stopped simulation and
> append?, If no could you please type the exact command I should use to
> solve the issue.
>
> Sincerely,
>
> Adarsh V. K.
> Research Scholar (PhD)
> National Institute of Technology, Calicut ( NIT C )
> Kerala state, India
>
> --
> On Thu, May 18, 2017 at 7:13 PM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > Some of your commands and outputs are inconsistent. You can't get
> > md_0_1.log without e.g. using -deffnm, and you'll only get md.log if you
> > don't use deffnm. But if you change that when trying to do your
> > continuation, mdrun won't know how to append because you haven't told it
> > that the old name. Be consistent. Your whole trajectory is present in all
> > your output files, but you're going to have to concatenate them yourself,
> > e.g. with gmx trjcat since you didn't tell mdrun a consistent name for
> the
> > files.
> >
> > GROMACS 2016 likely refuses to do your continuation, precisely so that
> you
> > are prompted to say what you actually want, rather than mdrun trying to
> be
> > clever and getting it wrong.
> >
> > Mark
> >
> > On Thu, May 18, 2017 at 11:03 AM Adarsh V. K. <
> adarsh_p13008...@nitc.ac.in>
> > wrote:
> >
> >> Dear gmx users,
> >>
> >> I use Gromacs 5.1.4 for protein ligand simulation. How can I restart a
> >> stopped simulation after a power failure? (used 8 processor cores +
> >> Graphics card GTX 780Ti).
> >>
> >> I have attached the log file along with this mail.
> >>
> >> It appeared that no details appended after restarting simulation (after
> >> power failure at 3.5 ns), Even Though the 'terminal' Ubuntu 16.04 shows
> >> that the simulation successfully restarted from 3.5 ns (used 8 processor
> >> cores + Graphics card GTX 780Ti) and completed the entire 8 ns
> >> simulation...!!. Frames...350 -> 3500 ps (not appended the log file
> after
> >> the restart from 3500ps to 8000ps).
> >>
> >> I used the command (gromacs 5.1.4),
> >>   # gmx mdrun -s md_0_1.tpr -cpi md_0_1_prev.cpt -v
> >>
> >> I also tried, # gmx mdrun -s md_0_1.tpr -cpi md_0_1_prev.cpt -append
> >>
> >> 
> >> 
> >> md_0_1.log : (final)
> >> -
> >> Step   Time Lambda
> >> 1765000 3530.00.0
> >>
> >>Energies (kJ/mol)
> >>G96AngleProper Dih.  Improper Dih.  LJ-14
> >> Coulomb-14
> >> 6.73096e+033.13198e+032.15931e+031.31375e+03
> >> 4.51549e+04
> >> LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
> >> Potential
> >> 3.66659e+05   -7.80170e+03   -2.71529e+064.12416e+03
> >> -2.29382e+06
> >> Kinetic En.   Total EnergyTemperature Pres. DC (bar) Pressure
> >> (bar)
> >> 4.12474e+05   -1.88135e+063.00209e+02   -7.62778e+01
> >> 2.10104e+01
> >>Constr. rmsd
> >> 2.37431e-05
> >> 
> >> -
> >> md.log (final)
> >> --
> >> Step   Time Lambda
> >> 400 8000.00.0
> >>
> >> Writing checkpoint, step 400 at Thu May 18 13:55:01 2017
> >>
> >>
> >>Energies (kJ/mol)
> >>G96AngleProper Dih.  Improper Dih.  LJ-14
> >> Coulomb-14
> >> 6.44959e+033.18212e+032.06343e+031.53953e+03
> >> 4.49878e+04
> >> LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
> >> Potential
> >> 3.66131e+05   -7.78489e+03   -2.71259e+064.78708e+03
> >> -2.29124e+06
> >> Kinetic En.   Total EnergyTemperature Pres. DC (bar) Pressure
> >> (bar)
> >> 4.13852e+05   -1.87738e+063.01212e+02   

[gmx-users] Can you please tell me the exact command? Re: Restart a stopped simulation after a power failure? : Not working in Gromacs 5.1.4

[Adarsh V. K.]

Dear Dr. Mark,

Thank you for the prompt reply. I have been struggling with the issue for
couple month time. Would you please advise me how to use  " -deffnm " flag
in commands?

# gmx mdrun  -s  md_0_1.tpr  -cpi  md_0_1_prev.cpt  -v  -deffnm

Will the above command will successful restart a stopped simulation and
append?, If no could you please type the exact command I should use to
solve the issue.

Sincerely,

Adarsh V. K.
Research Scholar (PhD)
National Institute of Technology, Calicut ( NIT C )
Kerala state, India

--
On Thu, May 18, 2017 at 7:13 PM, Mark Abraham 
wrote:

> Hi,
>
> Some of your commands and outputs are inconsistent. You can't get
> md_0_1.log without e.g. using -deffnm, and you'll only get md.log if you
> don't use deffnm. But if you change that when trying to do your
> continuation, mdrun won't know how to append because you haven't told it
> that the old name. Be consistent. Your whole trajectory is present in all
> your output files, but you're going to have to concatenate them yourself,
> e.g. with gmx trjcat since you didn't tell mdrun a consistent name for the
> files.
>
> GROMACS 2016 likely refuses to do your continuation, precisely so that you
> are prompted to say what you actually want, rather than mdrun trying to be
> clever and getting it wrong.
>
> Mark
>
> On Thu, May 18, 2017 at 11:03 AM Adarsh V. K. 
> wrote:
>
>> Dear gmx users,
>>
>> I use Gromacs 5.1.4 for protein ligand simulation. How can I restart a
>> stopped simulation after a power failure? (used 8 processor cores +
>> Graphics card GTX 780Ti).
>>
>> I have attached the log file along with this mail.
>>
>> It appeared that no details appended after restarting simulation (after
>> power failure at 3.5 ns), Even Though the 'terminal' Ubuntu 16.04 shows
>> that the simulation successfully restarted from 3.5 ns (used 8 processor
>> cores + Graphics card GTX 780Ti) and completed the entire 8 ns
>> simulation...!!. Frames...350 -> 3500 ps (not appended the log file after
>> the restart from 3500ps to 8000ps).
>>
>> I used the command (gromacs 5.1.4),
>>   # gmx mdrun -s md_0_1.tpr -cpi md_0_1_prev.cpt -v
>>
>> I also tried, # gmx mdrun -s md_0_1.tpr -cpi md_0_1_prev.cpt -append
>>
>> 
>> 
>> md_0_1.log : (final)
>> -
>> Step   Time Lambda
>> 1765000 3530.00.0
>>
>>Energies (kJ/mol)
>>G96AngleProper Dih.  Improper Dih.  LJ-14
>> Coulomb-14
>> 6.73096e+033.13198e+032.15931e+031.31375e+03
>> 4.51549e+04
>> LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>> Potential
>> 3.66659e+05   -7.80170e+03   -2.71529e+064.12416e+03
>> -2.29382e+06
>> Kinetic En.   Total EnergyTemperature Pres. DC (bar) Pressure
>> (bar)
>> 4.12474e+05   -1.88135e+063.00209e+02   -7.62778e+01
>> 2.10104e+01
>>Constr. rmsd
>> 2.37431e-05
>> 
>> -
>> md.log (final)
>> --
>> Step   Time Lambda
>> 400 8000.00.0
>>
>> Writing checkpoint, step 400 at Thu May 18 13:55:01 2017
>>
>>
>>Energies (kJ/mol)
>>G96AngleProper Dih.  Improper Dih.  LJ-14
>> Coulomb-14
>> 6.44959e+033.18212e+032.06343e+031.53953e+03
>> 4.49878e+04
>> LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>> Potential
>> 3.66131e+05   -7.78489e+03   -2.71259e+064.78708e+03
>> -2.29124e+06
>> Kinetic En.   Total EnergyTemperature Pres. DC (bar) Pressure
>> (bar)
>> 4.13852e+05   -1.87738e+063.01212e+02   -7.59495e+01
>> 5.34060e+01
>>Constr. rmsd
>> 2.33151e-05
>> -
>> Force evaluation time GPU/CPU: 12.005 ms/12.263 ms = 0.979
>> For optimal performance this ratio should be close to 1!
>>
>>Core t (s)   Wall t (s)(%)
>>Time:   312346.79739374.380  793.3
>>  10h56:14
>>  (ns/day)(hour/ns)
>> Performance:9.9672.408
>> Finished mdrun on rank 0 Thu May 18 13:55:02 2017
>>
>> 
>> ---
>> But while using the command it shows only 3.5 ns of simulation. How to
>> solve this problem
>>
>> gmx trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_0_1_noPBC.xtc -pbc mol -ur
>> compact
>>
>> Select 0 ("System")
>> 
>> -
>>
>> Later I repeated the whole 8 ns simulation from beginning It
>> completed with out any issues.
>>
>> Can any body tell me what happens during the power failure and why
>> 

Re: [gmx-users] Restart a stopped simulation after a power failure? : Not working in Gromacs 5.1.4

[Mark Abraham]

Hi,

Some of your commands and outputs are inconsistent. You can't get
md_0_1.log without e.g. using -deffnm, and you'll only get md.log if you
don't use deffnm. But if you change that when trying to do your
continuation, mdrun won't know how to append because you haven't told it
that the old name. Be consistent. Your whole trajectory is present in all
your output files, but you're going to have to concatenate them yourself,
e.g. with gmx trjcat since you didn't tell mdrun a consistent name for the
files.

GROMACS 2016 likely refuses to do your continuation, precisely so that you
are prompted to say what you actually want, rather than mdrun trying to be
clever and getting it wrong.

Mark

On Thu, May 18, 2017 at 11:03 AM Adarsh V. K. 
wrote:

> Dear gmx users,
>
> I use Gromacs 5.1.4 for protein ligand simulation. How can I restart a
> stopped simulation after a power failure? (used 8 processor cores +
> Graphics card GTX 780Ti).
>
> I have attached the log file along with this mail.
>
> It appeared that no details appended after restarting simulation (after
> power failure at 3.5 ns), Even Though the 'terminal' Ubuntu 16.04 shows
> that the simulation successfully restarted from 3.5 ns (used 8 processor
> cores + Graphics card GTX 780Ti) and completed the entire 8 ns
> simulation...!!. Frames...350 -> 3500 ps (not appended the log file after
> the restart from 3500ps to 8000ps).
>
> I used the command (gromacs 5.1.4),  mdrun -s md.tpr -cpi state.cpt
>
>   # gmx mdrun -s md_0_1.tpr -cpi md_0_1_prev.cpt -v
>
> I also tried, mdrun -s md.tpr -cpi state.cpt -append
>
>
> 
> md_0_1.log : (final)
> -
> Step   Time Lambda
> 1765000 3530.00.0
>
>Energies (kJ/mol)
>G96AngleProper Dih.  Improper Dih.  LJ-14 Coulomb-14
> 6.73096e+033.13198e+032.15931e+031.31375e+034.51549e+04
> LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.  Potential
> 3.66659e+05   -7.80170e+03   -2.71529e+064.12416e+03   -2.29382e+06
> Kinetic En.   Total EnergyTemperature Pres. DC (bar) Pressure (bar)
> 4.12474e+05   -1.88135e+063.00209e+02   -7.62778e+012.10104e+01
>Constr. rmsd
> 2.37431e-05
>
> -
> md.log (final)
> --
> Step   Time Lambda
> 400 8000.00.0
>
> Writing checkpoint, step 400 at Thu May 18 13:55:01 2017
>
>
>Energies (kJ/mol)
>G96AngleProper Dih.  Improper Dih.  LJ-14 Coulomb-14
> 6.44959e+033.18212e+032.06343e+031.53953e+034.49878e+04
> LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.  Potential
> 3.66131e+05   -7.78489e+03   -2.71259e+064.78708e+03   -2.29124e+06
> Kinetic En.   Total EnergyTemperature Pres. DC (bar) Pressure (bar)
> 4.13852e+05   -1.87738e+063.01212e+02   -7.59495e+015.34060e+01
>Constr. rmsd
> 2.33151e-05
> -
> Force evaluation time GPU/CPU: 12.005 ms/12.263 ms = 0.979
> For optimal performance this ratio should be close to 1!
>
>Core t (s)   Wall t (s)(%)
>Time:   312346.79739374.380  793.3
>  10h56:14
>  (ns/day)(hour/ns)
> Performance:9.9672.408
> Finished mdrun on rank 0 Thu May 18 13:55:02 2017
>
>
> ---
> But while using the command it shows only 3.5 ns of simulation. How to
> solve this problem
>
> gmx trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_0_1_noPBC.xtc -pbc mol -ur
> compact
>
> Select 0 ("System")
>
> -
>
> Later I repeated the whole 8 ns simulation from beginning It completed
> with out any issues.
>
> Can any body tell me what happens during the power failure and why
> re-starting a stopped simulation is not working.
>
> Is it any modification in 're-start' command is required?
>
> Regards,
> Adarsh V. K.
>
>
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Re: [gmx-users] md continuation

[Tasneem Kausar]

You can directly extend time with gmx covert-tpr -s old.tpr -o new.tpr
-extend 2

On 18 May 2017 15:34, "Kashif"  wrote:

> It means I should conver my md.mdp file for 40 ns from 20 ns in the same
> folder and then run this command ...
>
> grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md_0_1.tpr -extend
>
> after that this command...
>
> mdrun -deffnm md_0_1
>
> Please suggest the correct command if it is not correct.
>
> regards
>
> kashif
>
>
> On Wed, May 17, 2017 at 3:22 PM, Kashif 
> wrote:
>
> > I have already run my 20 ns md simulation of my protein. The log file is
> > showing completion of my 20 ns data. I have also done analysis by using
> > trjconv command and g_rms.
> > Now I want to increase my simulation at least for 20 ns more and make my
> > data of protein simulation for 40 ns. Kindly help for continuation of my
> > simulation. I have used this command but it did not help and shows error.
> > command:   mdrun -deffnm md_0_1 -cpi md_0_1.cpt -append
> >
> > error:
> > NOTE: 23 % of the run time was spent communicating energies,
> >   you might want to use the -gcom option of mdrun
> >
> >  Core t (s)Wall t (s)(%)
> >Time:   25.0002.843 879.2
> >   (ns/day)(hour/ns)
> > Performance:0.061  394.912
> > Finished mdrun on node 0 Sat Apr 29 11:46:36 2017
> >
> > regards
> > kashif
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
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Re: [gmx-users] ligand moving out during umbrella sampling

[Justin Lemkul]

On 5/17/17 8:55 AM, abhisek Mondal wrote:

This time I think I got ligand restrained successfully during the umbrella
sampling. I have removed the restrain from protein, as per your advice.
Defined the COM vector in md_umbrella.mdp, applied pull_k1=1000 and used
pull_rate1=0.0.
I have uploaded the trajectory movie (and other mdp files) in the following
link:
https://drive.google.com/drive/folders/0B6O-L5Y7BiGJQ1FIc2tIRFE2dE0

However, I'm facing a problem. Due to the withdrawal of the position
restrain of protein. The protein and ligand (together) is moving around the
box and resulting in "Distance of pull group 1 (10.441990 nm) is larger
than 0.49 times the box size (10.646989)" error.

As per the video I have uploaded, if I assume this approach worked, then
how can I avoid this error ? Is  there any way to make sure the
protein-ligand remains in the middle of the box (or nearby). I have taken
pretty large box compared to the protein structure from the beginning.

Please suggest me a way out.



Use a larger box or use direction-periodic geometry.

-Justin


On Mon, May 15, 2017 at 5:48 PM, Justin Lemkul  wrote:




On 5/15/17 2:45 AM, abhisek Mondal wrote:


On Thu, May 11, 2017 at 9:03 PM, Justin Lemkul  wrote:




On 5/11/17 9:21 AM, abhisek Mondal wrote:

On Thu, May 11, 2017 at 11:02 AM, abhisek Mondal  0
pull_vec1   = 0 0 -1


Note that with "direction" geometry, only pull_vec1 is acting.

pull_dim
is ignored.

The ligand was previously moving along x,y direction when I was using


pull_dim  = N N Y. So I changed it to Y in all direction and provided 0

as
vector  and pull_rate1=0.0, so that it does not move much. But at the
end
of a 10ns run, I see that the ligand is still moving as it was earlier.

It shows me:


 Pull group  natoms  pbc atom  distance at start reference at t=0
   0  1132936665
   159  1618  -1.555-1.555
Is it ok withe negative value ? Anyway this setup is not working.


Again you're trying to just apply the restraint to one dimension and it

looks to be fairly arbitrary.  I already suggested using the vector
connecting the ligand COM with the binding site residues' COM and using
that as pull_vec1.  Draw it out.  It makes a lot more sense than trying
to
restrain only along one axis, which as I have said before, makes no sense
in this case.

Thank you for such detailed suggestion.


I followed on as per your suggestion. Calculated COM of protein and
Ligand.
Calculated protein-lig vector (using COM) to be used for pulling (as
pull_vec1).
Pulling also achieved successfully.
But after pulling, when I performed the brief npt_umbrella run with
pull_rate1=0, I found the ligand is moving little bit. Could not
understand
what I have mistaken this time.
So I moved on for umbrella sampling mdrun step, with pull_rate1=0 and
pull_vec1=as determined from COM calculations. Despite I found that the
ligand is moving vigorously and got pulled away probably.
I'm putting npt_umbrella.mdp,md_umbrella.mdp,conf140.gro(used for
npt_umbrella), npt140.gro,md_umbrella run video in the following link:
https://drive.google.com/drive/folders/0B6O-L5Y7BiGJQ1FIc2tIRFE2dE0


Am I still missing some drastic steps ? Please suggest me if I do. I'm
totally lost here in this regard.



Again, don't restrain the protein.  I've said this multiple times.

The pull setup looks reasonable.  Maybe you just need a stronger force
constant, or you should not use the COM of the whole protein, instead the
COM of a few important residues (use an index group with gmx traj -ox -com
to get its coordinates).  If the specified vector is off, so too will be
the resulting biasing potential.

-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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* For 

Re: [gmx-users] Domain decomposition error

[Justin Lemkul]

On 5/18/17 5:59 AM, Kashif wrote:

I got this error every time when I try to simulate one of my protein-ligand
complex.

 ---
Program mdrun, VERSION 4.6.6
Source code file: /root/Documents/gromacs-4.6.6/src/mdlib/pme.c, line: 851

Fatal error:
1 particles communicated to PME node 5 are more than 2/3 times the cut-off
out of the domain decomposition cell of their charge group in dimension y.
This usually means that your system is not well equilibrated.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
...

Although, same parameters in mdp files fairly simulated the other
drug-protein complex. But this drug complex is creating trouble.
kindly help.



http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System

-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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Re: [gmx-users] md continuation

[Justin Lemkul]

On 5/18/17 6:04 AM, Kashif wrote:

It means I should conver my md.mdp file for 40 ns from 20 ns in the same
folder and then run this command ...

grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md_0_1.tpr -extend

after that this command...

mdrun -deffnm md_0_1

Please suggest the correct command if it is not correct.



No, because grompp does not have an -extend option and your mdrun command makes 
no reference to starting from an existing checkpoint file (with -cpi).  Read 
http://www.gromacs.org/Documentation/How-tos/Extending_Simulations carefully.


-Justin


regards

kashif


On Wed, May 17, 2017 at 3:22 PM, Kashif  wrote:


I have already run my 20 ns md simulation of my protein. The log file is
showing completion of my 20 ns data. I have also done analysis by using
trjconv command and g_rms.
Now I want to increase my simulation at least for 20 ns more and make my
data of protein simulation for 40 ns. Kindly help for continuation of my
simulation. I have used this command but it did not help and shows error.
command:   mdrun -deffnm md_0_1 -cpi md_0_1.cpt -append

error:
NOTE: 23 % of the run time was spent communicating energies,
  you might want to use the -gcom option of mdrun

 Core t (s)Wall t (s)(%)
   Time:   25.0002.843 879.2
  (ns/day)(hour/ns)
Performance:0.061  394.912
Finished mdrun on node 0 Sat Apr 29 11:46:36 2017

regards
kashif



--
==

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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Re: [gmx-users] Calculating number of molecules to add in simulation box

[Smith, Micholas D.]

0.67 moles/L * 2440.78 nm^3  = 0.67 moles* 2.4408*x10^-21

0.67*6.022141x10^23 molecules * 2.4408*x10^-21 = 0.67 * 1470 molecules

0.67 * 1470 = 984.9 molecules

You would need ~985 molecules in your box to fulfill your molar concentration.


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Pandya, Akash 

Sent: Thursday, May 18, 2017 8:52 AM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Calculating number of molecules to add in simulation box

Hi all,

I'm trying to calculate the number of Glycine molecules to add into the 
simulation box. The molar concentration of glycine I'm using is 0.67M. My 
simulation box size is 2nm and the box volume is 2440.78nm^3. How would I 
calculate the number of glycine molecules to fulfil this molar concentration?


Best wishes,

Akash

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[gmx-users] Calculating number of molecules to add in simulation box

[Pandya, Akash]

Hi all,

I'm trying to calculate the number of Glycine molecules to add into the 
simulation box. The molar concentration of glycine I'm using is 0.67M. My 
simulation box size is 2nm and the box volume is 2440.78nm^3. How would I 
calculate the number of glycine molecules to fulfil this molar concentration?


Best wishes,

Akash

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Re: [gmx-users] md continuation

[Kashif]

It means I should conver my md.mdp file for 40 ns from 20 ns in the same
folder and then run this command ...

grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md_0_1.tpr -extend

after that this command...

mdrun -deffnm md_0_1

Please suggest the correct command if it is not correct.

regards

kashif


On Wed, May 17, 2017 at 3:22 PM, Kashif  wrote:

> I have already run my 20 ns md simulation of my protein. The log file is
> showing completion of my 20 ns data. I have also done analysis by using
> trjconv command and g_rms.
> Now I want to increase my simulation at least for 20 ns more and make my
> data of protein simulation for 40 ns. Kindly help for continuation of my
> simulation. I have used this command but it did not help and shows error.
> command:   mdrun -deffnm md_0_1 -cpi md_0_1.cpt -append
>
> error:
> NOTE: 23 % of the run time was spent communicating energies,
>   you might want to use the -gcom option of mdrun
>
>  Core t (s)Wall t (s)(%)
>Time:   25.0002.843 879.2
>   (ns/day)(hour/ns)
> Performance:0.061  394.912
> Finished mdrun on node 0 Sat Apr 29 11:46:36 2017
>
> regards
> kashif
>
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[gmx-users] Domain decomposition error

[Kashif]

I got this error every time when I try to simulate one of my protein-ligand
complex.

 ---
Program mdrun, VERSION 4.6.6
Source code file: /root/Documents/gromacs-4.6.6/src/mdlib/pme.c, line: 851

Fatal error:
1 particles communicated to PME node 5 are more than 2/3 times the cut-off
out of the domain decomposition cell of their charge group in dimension y.
This usually means that your system is not well equilibrated.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
...

Although, same parameters in mdp files fairly simulated the other
drug-protein complex. But this drug complex is creating trouble.
kindly help.

regards
kashif
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[gmx-users] g_densmap with Cartesian coordinates results in segvault, cylindrical does not

[Vis, van der, J.S.]

Dear all,

I am having some trouble with using g_densmap in the Cartesian coordinate
system. I want to calculate the density over a cylindrical pore, where the
z-direction is the axial direction. The sideview works just fine using:

g_densmap -f hyper.trr -s hyper.tpr -n hyper.ndx -od densmap.dat -amax 10
-rmax 15 -b 10 -bin 0.05

and then defining the relevant index groups to get the right axial axis.
However, I also want to get a top-view of the pore, but this has less
success. No matter what I try, I get a segmentation fault. I know these are
hard to solve and that the problem is most likely somewhere in my
trajectory, but since the radial-axial calculation did work, I thought I
might have set some of the settings wrong. What I use is:

g_densmap -f hyper.trr -s hyper.tpr -n hyper.ndx -od densmap.dat -bin 0.05
-b 10 -xmin -10 -xmax 10 -d1 300 -d2 300

I assume right now that the reference position for g_densmap is the center
of the coordinate system and that d1 and d2 is also centered. Can you see
something that I'm doing wrong? I would appreciate any help!

Thank you,
Jaap
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[gmx-users] Restart a stopped simulation after a power failure? : Not working in Gromacs 5.1.4

[Adarsh V. K.]

Dear gmx users,

I use Gromacs 5.1.4 for protein ligand simulation. How can I restart a
stopped simulation after a power failure? (used 8 processor cores +
Graphics card GTX 780Ti).

I have attached the log file along with this mail.

It appeared that no details appended after restarting simulation (after
power failure at 3.5 ns), Even Though the 'terminal' Ubuntu 16.04 shows
that the simulation successfully restarted from 3.5 ns (used 8 processor
cores + Graphics card GTX 780Ti) and completed the entire 8 ns
simulation...!!. Frames...350 -> 3500 ps (not appended the log file after
the restart from 3500ps to 8000ps).

I used the command (gromacs 5.1.4),  mdrun -s md.tpr -cpi state.cpt

  # gmx mdrun -s md_0_1.tpr -cpi md_0_1_prev.cpt -v

I also tried, mdrun -s md.tpr -cpi state.cpt -append


md_0_1.log : (final)
-
Step   Time Lambda
1765000 3530.00.0

   Energies (kJ/mol)
   G96AngleProper Dih.  Improper Dih.  LJ-14 Coulomb-14
6.73096e+033.13198e+032.15931e+031.31375e+034.51549e+04
LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.  Potential
3.66659e+05   -7.80170e+03   -2.71529e+064.12416e+03   -2.29382e+06
Kinetic En.   Total EnergyTemperature Pres. DC (bar) Pressure (bar)
4.12474e+05   -1.88135e+063.00209e+02   -7.62778e+012.10104e+01
   Constr. rmsd
2.37431e-05
-
md.log (final)
--
Step   Time Lambda
400 8000.00.0

Writing checkpoint, step 400 at Thu May 18 13:55:01 2017


   Energies (kJ/mol)
   G96AngleProper Dih.  Improper Dih.  LJ-14 Coulomb-14
6.44959e+033.18212e+032.06343e+031.53953e+034.49878e+04
LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.  Potential
3.66131e+05   -7.78489e+03   -2.71259e+064.78708e+03   -2.29124e+06
Kinetic En.   Total EnergyTemperature Pres. DC (bar) Pressure (bar)
4.13852e+05   -1.87738e+063.01212e+02   -7.59495e+015.34060e+01
   Constr. rmsd
2.33151e-05
-
Force evaluation time GPU/CPU: 12.005 ms/12.263 ms = 0.979
For optimal performance this ratio should be close to 1!

   Core t (s)   Wall t (s)(%)
   Time:   312346.79739374.380  793.3
 10h56:14
 (ns/day)(hour/ns)
Performance:9.9672.408
Finished mdrun on rank 0 Thu May 18 13:55:02 2017

---
But while using the command it shows only 3.5 ns of simulation. How to
solve this problem

gmx trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_0_1_noPBC.xtc -pbc mol -ur
compact

Select 0 ("System")

-

Later I repeated the whole 8 ns simulation from beginning It completed
with out any issues.

Can any body tell me what happens during the power failure and why
re-starting a stopped simulation is not working.

Is it any modification in 're-start' command is required?

Regards,
Adarsh V. K.
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