Re: [gmx-users] Small molecule parametrization

[sun.iba2]

This is a small molecule with dicyanovinyl group substituted at para position 
on one of the phenyl ring. I suspect the charges are not proper because in ATB 
the group charges must be -1,0 or 1. For some groups charges are summed up to 
zero but this is not the case of all groups. 


Sent from Samsung Mobile

 Original message From: Justin Lemkul 
 Date:09/09/2016  5:18 AM  (GMT+05:30) 
To: gmx-us...@gromacs.org Cc:  Subject: Re: 
[gmx-users] Small molecule parametrization 


On 9/7/16 1:43 PM, Sun Iba wrote:
> Hi
> I have parametreized my small molecule with the help of ATB server. I have
> learnt that ATB provides GROMOS charges better than PRODRG. However, I have
> serious doubts regarding the charges assigned to hydrophobic groups. Also I
> need to convert the calculated charges into GROMOS 43a1 set (force field I
> am using). I am pasting the .itp file produced by ATB:
>
> nr  type  resnr  resid  atom  cgnr  chargemasstotal_charge
> 1   CH31SCX1C1210.223  15.0350
> 2OE1SCX1 O11   -0.275  15.9994 ; -0.052
> 3 C1SCX1 C320.476  12.0110
> 4 C1SCX1 C22   -0.157  12.0110
> 5 C1SCX1 C42   -0.376  12.0110
> 6HC1SCX1 H220.172   1.0080 ;  0.115
> 7 C1SCX1 C630.095  12.0110
> 8HC1SCX1 H430.137   1.0080
> 9 C1SCX1 C93   -0.386  12.0110
>10 C1SCX1C1330.478  12.0110
>11NR1SCX1 N23   -0.525  14.0067 ; -0.201
>12 C1SCX1C1940.539  12.0110
>13NR1SCX1 N44   -0.539  14.0067 ;  0.000
>14 C1SCX1 C15   -0.117  12.0110
>15HC1SCX1 H150.157   1.0080
>16 C1SCX1 C55   -0.150  12.0110
>17HC1SCX1 H350.131   1.0080 ;  0.021
>18 C1SCX1 C760.097  12.0110
>19 C1SCX1C1160.247  12.0110
>20HC1SCX1 H660.079   1.0080
>21NR1SCX1 N16   -0.423  14.0067 ;  0.000
>22NT1SCX1 N370.171  14.0067
>23 C1SCX1C1670.387  12.0110
>24 O1SCX1 O27   -0.492  15.9994
>25 C1SCX1C1870.495  12.0110
>26 F1SCX1 F17   -0.187  18.9984
>27 F1SCX1 F27   -0.187  18.9984
>28 F1SCX1 F37   -0.187  18.9984 ;  0.000
>29 C1SCX1C158   -0.211  12.0110
>30 C1SCX1C1480.388  12.0110
>31   CH31SCX1C108   -0.060  15.0350 ;  0.117
>32 C1SCX1C229   -0.444  12.0110
>33HC1SCX1H1190.187   1.0080
>34 C1SCX1C2190.309  12.0110
>35   CH31SCX1 C89   -0.052  15.0350 ;  0.000
>36 C1SCX1C20   10   -0.340  12.0110
>37HC1SCX1H10   100.226   1.0080
>38 C1SCX1C17   10   -0.026  12.0110
>39HC1SCX1 H8   100.140   1.0080 ;  0.000
>

What is this molecule and why do you think the charges are inappropriate?

>
> Please have a look and help me understanding if the charges are too bad.
> Also my Nitrogen atom is not aromatic. It is linked to C by triple bond and
> to another N by double bond. Does GROMOS treat this type of nitrogn as NT
> and NR?
>

N can't be linked to one atom via triple bond and another via double bond. 
That's five bonds.  Unless your N has expanded its valence into d-orbitals, 
that's not going to be possible.

-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

==
-- 
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.
-- 
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 

Re: [gmx-users] Small molecule parametrization

[sun.iba2]

I am sorry i dint explain it nicely. One N i.e  NT is linked to one N via 
single bond and to another Carbon via single bond(C=N-N-C) . And second N atom 
i.e. N2 is linked to one Carbon (as CN). ATB treated the former N atom as NT 
and and later N atom as NR.


Sent from Samsung Mobile

 Original message From: Justin Lemkul 
 Date:09/09/2016  5:18 AM  (GMT+05:30) 
To: gmx-us...@gromacs.org Cc:  Subject: Re: 
[gmx-users] Small molecule parametrization 


On 9/7/16 1:43 PM, Sun Iba wrote:
> Hi
> I have parametreized my small molecule with the help of ATB server. I have
> learnt that ATB provides GROMOS charges better than PRODRG. However, I have
> serious doubts regarding the charges assigned to hydrophobic groups. Also I
> need to convert the calculated charges into GROMOS 43a1 set (force field I
> am using). I am pasting the .itp file produced by ATB:
>
> nr  type  resnr  resid  atom  cgnr  chargemasstotal_charge
> 1   CH31SCX1C1210.223  15.0350
> 2OE1SCX1 O11   -0.275  15.9994 ; -0.052
> 3 C1SCX1 C320.476  12.0110
> 4 C1SCX1 C22   -0.157  12.0110
> 5 C1SCX1 C42   -0.376  12.0110
> 6HC1SCX1 H220.172   1.0080 ;  0.115
> 7 C1SCX1 C630.095  12.0110
> 8HC1SCX1 H430.137   1.0080
> 9 C1SCX1 C93   -0.386  12.0110
>10 C1SCX1C1330.478  12.0110
>11NR1SCX1 N23   -0.525  14.0067 ; -0.201
>12 C1SCX1C1940.539  12.0110
>13NR1SCX1 N44   -0.539  14.0067 ;  0.000
>14 C1SCX1 C15   -0.117  12.0110
>15HC1SCX1 H150.157   1.0080
>16 C1SCX1 C55   -0.150  12.0110
>17HC1SCX1 H350.131   1.0080 ;  0.021
>18 C1SCX1 C760.097  12.0110
>19 C1SCX1C1160.247  12.0110
>20HC1SCX1 H660.079   1.0080
>21NR1SCX1 N16   -0.423  14.0067 ;  0.000
>22NT1SCX1 N370.171  14.0067
>23 C1SCX1C1670.387  12.0110
>24 O1SCX1 O27   -0.492  15.9994
>25 C1SCX1C1870.495  12.0110
>26 F1SCX1 F17   -0.187  18.9984
>27 F1SCX1 F27   -0.187  18.9984
>28 F1SCX1 F37   -0.187  18.9984 ;  0.000
>29 C1SCX1C158   -0.211  12.0110
>30 C1SCX1C1480.388  12.0110
>31   CH31SCX1C108   -0.060  15.0350 ;  0.117
>32 C1SCX1C229   -0.444  12.0110
>33HC1SCX1H1190.187   1.0080
>34 C1SCX1C2190.309  12.0110
>35   CH31SCX1 C89   -0.052  15.0350 ;  0.000
>36 C1SCX1C20   10   -0.340  12.0110
>37HC1SCX1H10   100.226   1.0080
>38 C1SCX1C17   10   -0.026  12.0110
>39HC1SCX1 H8   100.140   1.0080 ;  0.000
>

What is this molecule and why do you think the charges are inappropriate?

>
> Please have a look and help me understanding if the charges are too bad.
> Also my Nitrogen atom is not aromatic. It is linked to C by triple bond and
> to another N by double bond. Does GROMOS treat this type of nitrogn as NT
> and NR?
>

N can't be linked to one atom via triple bond and another via double bond. 
That's five bonds.  Unless your N has expanded its valence into d-orbitals, 
that's not going to be possible.

-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

==
-- 
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.
-- 
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] Free energy calculation, Methane in water tutorial

[sun.iba2]

Yes. I am doing that now. Thank you  ery much.


Sent from Samsung Mobile

 Original message From: Justin Lemkul 
<jalem...@vt.edu> Date:02/09/2016  8:01 PM  (GMT+05:30) 
To: gmx-us...@gromacs.org Cc:  Subject: Re: 
[gmx-users] Free energy calculation, Methane in water tutorial 


On 9/2/16 9:53 AM, sun.iba2 wrote:
> Yes. But nothing else is printed on screen. Log files are creared but 
> incomplete. When I used perl script to generate respective .mdp files for 
> mininization and equilibrium, i found all of the generated files for 21 
> lambda values were empty. However when I tried with my molecule, the 21 .mdp 
> files are created properly but still encountered same error with my file i.e. 
> .tpr file is missing.
>

This suggests something at the very top level is not set up correctly (paths, 
environment variables, etc).  Run the commands in the job script interactively 
to figure out which step is failing.

-Justin

>
>
>
>
>  Original message From: Justin Lemkul 
> <jalem...@vt.edu> Date:02/09/2016  4:57 PM  (GMT+05:30) 
> To: gmx-us...@gromacs.org Cc:  Subject: Re: 
> [gmx-users] Free energy calculation, Methane in water tutorial 
> 
>
> On 9/2/16 7:09 AM, Sun Iba wrote:
>> Hello dear users
>>
>> I am following Justin's tutorial for free energy calculation of Methane in
>> water. I have downloaded the job.sh file and trying to run it in terminal
>> using: sh job.sh but it is giving following error:
>>
>> Program mdrun, VERSION 5.0
>> Source code file:
>> /home/corona2/Downloads/gromacs-5.0/src/gromacs/fileio/gmxfio.c, line: 513
>>
>> Can not open file:
>> min0.tpr
>> For more information and tips for troubleshooting, please check the GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>> ---
>>
>> Please help me with error.
>>
>
> grompp failed to produce the .tpr file.  Use the screen output to figure out 
> why.
>
> -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

==
-- 
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.
-- 
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] Free energy calculation, Methane in water tutorial

[sun.iba2]

Yes. Doing that. Thank you very much.


Sent from Samsung Mobile

 Original message From: Nikhil Maroli 
 Date:02/09/2016  7:28 PM  (GMT+05:30) 
To: gromacs.org_gmx-users@maillist.sys.kth.se Cc:  
Subject: Re: [gmx-users] Free energy calculation, Methane in water 
tutorial 
run the single code from script and see what prints on the screen,that's
what Justin suggested
-- 
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.
-- 
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] Free energy calculation, Methane in water tutorial

[sun.iba2]

@Gozde..yes the.tpr file is not produced. I am looking at it. Will try again.
Thank you


Sent from Samsung Mobile

 Original message From: gozde ergin 
 Date:02/09/2016  4:56 PM  (GMT+05:30) 
To: gmx-us...@gromacs.org Cc:  Subject: Re: 
[gmx-users] Free energy calculation, Methane in water tutorial 
The error is pretty clear. Do you produce the min0.tpr file?
Where do you put this file? Is it in the same directory of job.sh file?

> On 02 Sep 2016, at 13:09, Sun Iba  wrote:
> 
> Hello dear users
> 
> I am following Justin's tutorial for free energy calculation of Methane in
> water. I have downloaded the job.sh file and trying to run it in terminal
> using: sh job.sh but it is giving following error:
> 
> Program mdrun, VERSION 5.0
> Source code file:
> /home/corona2/Downloads/gromacs-5.0/src/gromacs/fileio/gmxfio.c, line: 513
> 
> Can not open file:
> min0.tpr
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ---
> 
> Please help me with error.
> -- 
> 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.

-- 
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.
-- 
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] Free energy calculation, Methane in water tutorial

[sun.iba2]

Yes. But nothing else is printed on screen. Log files are creared but 
incomplete. When I used perl script to generate respective .mdp files for 
mininization and equilibrium, i found all of the generated files for 21 lambda 
values were empty. However when I tried with my molecule, the 21 .mdp files are 
created properly but still encountered same error with my file i.e. .tpr file 
is missing. 





 Original message From: Justin Lemkul 
 Date:02/09/2016  4:57 PM  (GMT+05:30) 
To: gmx-us...@gromacs.org Cc:  Subject: Re: 
[gmx-users] Free energy calculation, Methane in water tutorial 


On 9/2/16 7:09 AM, Sun Iba wrote:
> Hello dear users
>
> I am following Justin's tutorial for free energy calculation of Methane in
> water. I have downloaded the job.sh file and trying to run it in terminal
> using: sh job.sh but it is giving following error:
>
> Program mdrun, VERSION 5.0
> Source code file:
> /home/corona2/Downloads/gromacs-5.0/src/gromacs/fileio/gmxfio.c, line: 513
>
> Can not open file:
> min0.tpr
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ---
>
> Please help me with error.
>

grompp failed to produce the .tpr file.  Use the screen output to figure out 
why.

-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

==
-- 
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.
-- 
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] extending simulation

[sun.iba2]

You must have provided 5 for -extend flag in convert-tpr. Right? Then It 
should work. Start your mdrun with new.tpr. 
Or if it does not work, try changing the .mdp file options and adjust those. 
Recently I posted similar query and Dr. Lemkul replied. Please find that thread 
in the mailing list. The mail will redirect you to "How to extend simulation" 
page of Gromacs.
May I know why you don't have checkpoint file.
Best Wishes
Suniba


Sent from Samsung Mobile

 Original message From: Neha Gandhi 
 Date:10/08/2016  1:32 PM  (GMT+05:30) 
To: Discussion list for GROMACS users  
Cc:  Subject: [gmx-users] extending simulation 
Dear List,

I have only .xtc, .edr, .top and .tpr files. I want to extend my runs. I
tried converting .xtc to .trr. Then I tried using both grompp and/or
convert-tpr tools to extend my runs as recommended by gromacs manual.

However, when I input new tpr file to mdrun it starts the run with time=0
ps. I want the simulation to start with t=50 ns after previous run.

Is there a way to work around this without .cpt file?

Regards,
Neha
-- 
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.
-- 
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] Time frames missing

[sun.iba2]

Dear Sir

Is there a way to start from 159 ns and end it at 166 without checkpoint file. 
Because no checkpoint is there, neither it is backed up. The log file is 
updated till 161ns and when i give state.cpt, the fatal error occurs with the 
follwing msg:
 
Cannot find log file of 145900 kb. 

The information in .trr says that frames till 159 ns are present but the .log 
file is updated till 161.. And that is also incomplete.


Is there a ways to continue from 159 ..otherwise i will start from 100 ns 
again. 

 Original message From: Justin Lemkul 
 Date:02/08/2016  3:12 AM  (GMT+05:30) 
To: gmx-us...@gromacs.org Cc:  Subject: Re: 
[gmx-users] Time frames missing 


On 8/1/16 2:41 AM, Sun Iba wrote:
> Hello everyone
>
> I have extended a 100 ns simulation of a protein in water up to 200 ns.
> However, the system kept shutting down during the course of simulation and
> i had to restart the runs twice. Following are the files I obtained after
> completion of mdrun (I am writing information of .xtc only, for .trr its
> same:
>
>
> *md_0_1.xtc = 0 to 100 ns*
>
> *new.xtc = 99.990 to 159.990*
>
> *v.xtc = 166.050 to 179.050*
> *traj-comp.xtc = 179.620 to 200.00 ns*
>
> Now I am surprised to see that the time frames from 159.990 to 166.050 are
> not written to any file. I have also checked the .trr and .xtc file with
> gmx check and found that time frames are incomplete after the follwoing
> command:
>
>  gmx check -f new.trr
>
> Checking file new.trr
> trn version: GMX_trn_file (single precision)
> Reading frame   0 time 0.000
> # Atoms  133688
> Reading frame6000 time 159990.000
>
> *WARNING: Incomplete frame: nr 6607 time 166060*
>
> Item#frames Timestep (ps)
> Step  660710
> Time  660710
> Lambda660710
> Coords660710
> Velocities660710
> Forces   0
> Box   660710
>
> Now I am not sure to catenate the avaialble file or should i start the run
> again from 159.990 to 166.050? iF YES, WHAT WOULD BE THE COMMAND FOR THAT...
>

http://www.gromacs.org/Documentation/How-tos/Doing_Restarts

-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

==
-- 
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.
-- 
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] Time frames missing

[sun.iba2]

Thank you Sir but this is the first thing I looked at. Actually the checkpoint 
file is also missing. 


Sent from Samsung Mobile

 Original message From: Justin Lemkul 
 Date:02/08/2016  3:12 AM  (GMT+05:30) 
To: gmx-us...@gromacs.org Cc:  Subject: Re: 
[gmx-users] Time frames missing 


On 8/1/16 2:41 AM, Sun Iba wrote:
> Hello everyone
>
> I have extended a 100 ns simulation of a protein in water up to 200 ns.
> However, the system kept shutting down during the course of simulation and
> i had to restart the runs twice. Following are the files I obtained after
> completion of mdrun (I am writing information of .xtc only, for .trr its
> same:
>
>
> *md_0_1.xtc = 0 to 100 ns*
>
> *new.xtc = 99.990 to 159.990*
>
> *v.xtc = 166.050 to 179.050*
> *traj-comp.xtc = 179.620 to 200.00 ns*
>
> Now I am surprised to see that the time frames from 159.990 to 166.050 are
> not written to any file. I have also checked the .trr and .xtc file with
> gmx check and found that time frames are incomplete after the follwoing
> command:
>
>  gmx check -f new.trr
>
> Checking file new.trr
> trn version: GMX_trn_file (single precision)
> Reading frame   0 time 0.000
> # Atoms  133688
> Reading frame6000 time 159990.000
>
> *WARNING: Incomplete frame: nr 6607 time 166060*
>
> Item#frames Timestep (ps)
> Step  660710
> Time  660710
> Lambda660710
> Coords660710
> Velocities660710
> Forces   0
> Box   660710
>
> Now I am not sure to catenate the avaialble file or should i start the run
> again from 159.990 to 166.050? iF YES, WHAT WOULD BE THE COMMAND FOR THAT...
>

http://www.gromacs.org/Documentation/How-tos/Doing_Restarts

-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

==
-- 
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.
-- 
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.