[gmx-users] RMSF

[YanhuaOuyang]

Dear gromacs users,
I have run a MD of 2 short peptides respectively, I want to compare the 
flexibility between these two peptides along the full sequence via the 
per-residue RMSF.
I understand that gmx rmsf computes the root mean square fluctuation of atomic 
positions in the trajectory (supplied with -f) after(optionally) fitting to a 
reference frame (supplied with -s), namely using "fit" option. Well, I am 
confused that if we add "nofit" option when calculating RMSF, does gmx rmsf 
still fit before computing rms flucuation? If so, what structure does gmx rmsf 
fit to since no fitting to reference structure(supplied with -s)?

Best regards,
Ouyang
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] Questions on residue RMSF

[YanhuaOuyang]

Dear gromacs users,
I have run a MD of 2 short peptides respectively, I want to compare the 
flexibility between these two peptides along the full sequence via the 
per-residue RMSF.

I wonder that should I use "nofit" of "fit" option when I calculate the 
per-residue RMSF of a trajectory using gmx rmsf ? What is the difference 
between using "fit" and "nofit" option?


Best regards,
Ouyang
-- 
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] set computer time on REMD simulation

[YanhuaOuyang]

Sorry, it seems that I did not express my problem clearly.
I add "-maxh 0.1", it should be terminated until 10 minutes maximumly. However, 
the MD did not stop after over one hour.








At 2017-12-18 15:48:10, "Qinghua Liao" <scorpio.l...@gmail.com> wrote:
>Hello,
>
>If I understand correctly, it terminates at 0.99*t, t is the time you 
>set in hour.
>In you case, you simulation should be terminated at 0.1*0.99 = 0.099 h, 
>which is 5.94 minutes.
>
>PS: 0.1 h is not 10 minutes, but 6 minutes.
>
>All the best,
>Qinghua
>
>On 12/18/2017 08:05 AM, YanhuaOuyang wrote:
>> Dear gromacs user,
>>  The computing workstation I used has a limited time: 6 hours, 
>> namely the  REMD will be terminated after 6 hours. So I add option "-maxh 
>> 0.1" in the MD commands to test. The md commands are  as below:
>>   mdrun_mpi  -s remd_.tpr -multi 20 -replex 1000  -x remd_.xtc -cpo 
>> remd_.cpt -e remd_.edr -g remd_.log -c remd_.gro -maxh 0.1
>>
>> However the REMD did not terminate after the test time, 10 minutes.
>> Why the option "-maxh 0.1" did not work?
>> How to solve the limited time problem?
>>
>> Ouyang,
>> Best regards
>
>-- 
>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.

[gmx-users] set computer time on REMD simulation

[YanhuaOuyang]

Dear gromacs user,
The computing workstation I used has a limited time: 6 hours, namely 
the  REMD will be terminated after 6 hours. So I add option "-maxh 0.1" in the 
MD commands to test. The md commands are  as below:
 mdrun_mpi  -s remd_.tpr -multi 20 -replex 1000  -x remd_.xtc -cpo remd_.cpt -e 
remd_.edr -g remd_.log -c remd_.gro -maxh 0.1

However the REMD did not terminate after the test time, 10 minutes.
Why the option "-maxh 0.1" did not work?
How to solve the limited time problem?

Ouyang,
Best regards
-- 
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] Problem on continuing MD

[YanhuaOuyang]

Dear Mark,


Thank you so much. I have read the linked website you told and know why such 
problem happens.


Best regards,
Ouyang 








At 2017-11-01 17:39:17, "Mark Abraham" <mark.j.abra...@gmail.com> wrote:
>Hi,
>
>See http://www.gromacs.org/Documentation/Terminology/Reproducibility. You
>have non-reproducible load balancing. However this is not a problem unless
>your experimental design hinges upon being able to reproduce an exact
>trajectory (in which case you will have a tough time getting performance).
>You would get a different trajectory if you rotated your initial system by
>90 degrees too. Which one is "right?"
>
>Mark
>
>On Wed, Nov 1, 2017 at 10:20 AM YanhuaOuyang <15901283...@163.com> wrote:
>
>> Dear gromacs user,
>>
>>
>>Today, I continue the MD twice in two directories from the same
>> point of the MD trajectory, for example 100ns, using the same CPU, same
>> checkpoint file, same serve node. To my surprise, the energy informations
>> are different between the two continued log ouput files, which are shown
>> below.
>>
>>
>> continue_md_01.log:
>>
>> Started mdrun on rank 0 Wed Nov  1 23:17:08 2017
>>
>>Step   Time Lambda
>>
>>5000   10.00.0
>>
>>Energies (kJ/mol)
>>
>>BondU-BProper Dih.  Improper Dih.  CMAP Dih.
>>
>> 4.67507e+021.47390e+031.44019e+036.93280e+018.29478e+01
>>
>>   LJ-14 Coulomb-14LJ (SR)  Disper. corr.   Coulomb (SR)
>>
>> 4.17297e+029.82076e+031.12930e+05   -8.68735e+03   -1.15522e+06
>>
>>Coul. recip.  PotentialKinetic En.   Total Energy  Conserved En.
>>
>> 5.88613e+03   -1.03132e+061.63796e+05   -8.67527e+05   -1.90771e+05
>>
>> Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>>
>> 2.82366e+02   -2.04258e+02   -7.74514e+022.31539e-06
>>
>> DD  step 5019 load imb.: force 29.5%  pme mesh/force 0.964
>>
>> At step 5020 the performance loss due to force load imbalance is 11.1 %
>>
>>Step   Time Lambda
>>
>>50001000   12.00.0
>>
>>Energies (kJ/mol)
>>
>>BondU-BProper Dih.  Improper Dih.  CMAP Dih.
>>
>> 4.65447e+021.50124e+031.50444e+037.92082e+011.64421e+01
>>
>>   LJ-14 Coulomb-14LJ (SR)  Disper. corr.   Coulomb (SR)
>>
>> 4.18616e+029.80230e+031.11198e+05   -8.68735e+03   -1.15433e+06
>>
>>Coul. recip.  PotentialKinetic En.   Total Energy  Conserved En.
>>
>> 5.95908e+03   -1.03208e+061.64017e+05   -8.68059e+05   -1.90761e+05
>>
>> Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>>
>> 2.82747e+02   -2.04258e+02   -9.31332e+023.06123e-06
>>
>> DD  step 50001999  vol min/aver 0.880  load imb.: force 10.0%  pme
>> mesh/force 1.059
>>
>> ...
>>
>>
>>
>>
>> continue_md_02.log:
>>
>> Started mdrun on rank 0 Wed Nov  1 23:39:51 2017
>>
>>Step   Time Lambda
>>
>>5000   10.00.0
>>
>>Energies (kJ/mol)
>>
>>BondU-BProper Dih.  Improper Dih.  CMAP Dih.
>>
>> 4.67507e+021.47390e+031.44019e+036.93280e+018.29478e+01
>>
>>   LJ-14 Coulomb-14LJ (SR)  Disper. corr.   Coulomb (SR)
>>
>> 4.17297e+029.82076e+031.12930e+05   -8.68735e+03   -1.15522e+06
>>
>>Coul. recip.  PotentialKinetic En.   Total Energy  Conserved En.
>>
>> 5.88613e+03   -1.03132e+061.63796e+05   -8.67527e+05   -1.90771e+05
>>
>> Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>>
>> 2.82366e+02   -2.04258e+02   -7.74505e+022.31539e-06
>>
>> DD  step 5019 load imb.: force 18.3%  pme mesh/force 0.950
>>
>> At step 5020 the performance loss due to force load imbalance is 6.9 %
>>
>>Step   Time Lambda
>>
>>50001000   12.00.0
>>
>>Energies (kJ/mol)
>>
>>BondU-BProper Dih.  Improper Dih.  CMAP Dih.
>>
>> 4.51321e+021.43914e+031.56368e+039.15439e+011.64274e+01
>>
>>   LJ-14 Coulomb-14L

[gmx-users] Problem on continuing MD

[YanhuaOuyang]

Dear gromacs user,


   Today, I continue the MD twice in two directories from the same point of 
the MD trajectory, for example 100ns, using the same CPU, same checkpoint file, 
same serve node. To my surprise, the energy informations are different between 
the two continued log ouput files, which are shown below. 


continue_md_01.log:

Started mdrun on rank 0 Wed Nov  1 23:17:08 2017

   Step   Time Lambda

   5000   10.00.0

   Energies (kJ/mol)

   BondU-BProper Dih.  Improper Dih.  CMAP Dih.

4.67507e+021.47390e+031.44019e+036.93280e+018.29478e+01

  LJ-14 Coulomb-14LJ (SR)  Disper. corr.   Coulomb (SR)

4.17297e+029.82076e+031.12930e+05   -8.68735e+03   -1.15522e+06

   Coul. recip.  PotentialKinetic En.   Total Energy  Conserved En.

5.88613e+03   -1.03132e+061.63796e+05   -8.67527e+05   -1.90771e+05

Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd

2.82366e+02   -2.04258e+02   -7.74514e+022.31539e-06

DD  step 5019 load imb.: force 29.5%  pme mesh/force 0.964

At step 5020 the performance loss due to force load imbalance is 11.1 %

   Step   Time Lambda

   50001000   12.00.0

   Energies (kJ/mol)

   BondU-BProper Dih.  Improper Dih.  CMAP Dih.

4.65447e+021.50124e+031.50444e+037.92082e+011.64421e+01

  LJ-14 Coulomb-14LJ (SR)  Disper. corr.   Coulomb (SR)

4.18616e+029.80230e+031.11198e+05   -8.68735e+03   -1.15433e+06

   Coul. recip.  PotentialKinetic En.   Total Energy  Conserved En.

5.95908e+03   -1.03208e+061.64017e+05   -8.68059e+05   -1.90761e+05

Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd

2.82747e+02   -2.04258e+02   -9.31332e+023.06123e-06

DD  step 50001999  vol min/aver 0.880  load imb.: force 10.0%  pme mesh/force 
1.059

...




continue_md_02.log:

Started mdrun on rank 0 Wed Nov  1 23:39:51 2017

   Step   Time Lambda

   5000   10.00.0

   Energies (kJ/mol)

   BondU-BProper Dih.  Improper Dih.  CMAP Dih.

4.67507e+021.47390e+031.44019e+036.93280e+018.29478e+01

  LJ-14 Coulomb-14LJ (SR)  Disper. corr.   Coulomb (SR)

4.17297e+029.82076e+031.12930e+05   -8.68735e+03   -1.15522e+06

   Coul. recip.  PotentialKinetic En.   Total Energy  Conserved En.

5.88613e+03   -1.03132e+061.63796e+05   -8.67527e+05   -1.90771e+05

Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd

2.82366e+02   -2.04258e+02   -7.74505e+022.31539e-06

DD  step 5019 load imb.: force 18.3%  pme mesh/force 0.950

At step 5020 the performance loss due to force load imbalance is 6.9 %

   Step   Time Lambda

   50001000   12.00.0

   Energies (kJ/mol)

   BondU-BProper Dih.  Improper Dih.  CMAP Dih.

4.51321e+021.43914e+031.56368e+039.15439e+011.64274e+01

  LJ-14 Coulomb-14LJ (SR)  Disper. corr.   Coulomb (SR)

4.07426e+029.84156e+031.12168e+05   -8.68735e+03   -1.15440e+06

   Coul. recip.  PotentialKinetic En.   Total Energy  Conserved En.

5.88309e+03   -1.03123e+061.62769e+05   -8.68456e+05   -1.90745e+05

Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd

2.80597e+02   -2.04258e+02   -8.80279e+022.64599e-06

DD  step 50001999  vol min/aver 0.905  load imb.: force 32.7%  pme mesh/force 
1.034

   ...




It is obviously shown that the energy informations varied from 12ps (the md 
is continued from 100ns). Generally speaking, the two continued MD should be 
same each other since the conditions are same.
Why are they different? Does it mean the MD can not be terminated or transfered 
from one server to another because they are changeable if we want to 
investigate the dynamic property?
Do anyone knows the problems?




Best regards,
Ouyang.






-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] question about gmx do_dssp

[YanhuaOuyang]

Hi,
   I have run a MD simulation and used gmx do_dssp to calculate the secondary 
structure content. The output files are md_dssp.xpm and scount.xvg. I want to 
know that each residue  belongs to what kind of secondary structure for each 
frame. But the scount.xvg output file only have the number of residues with 
each secondary structure and the total secondary structure count as a function 
of time. So,  can I get the information on "each residue belongs to which kind 
of secondary structure for each frame" to draw a figure of " amino acid vs 
secondary structure" ?

Best regards,
Ouyang
-- 
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] Question on force field

[YanhuaOuyang]

Dear Justin,  Thank you very much. I get it now.Best 
regards,Ouyang
At 2017-07-31 10:46:10, "Justin Lemkul" <jalem...@vt.edu> wrote:
>
>
>On 7/30/17 8:58 PM, YanhuaOuyang wrote:
>> Hi,
>>   I have run a protein MD simulation and choose a force field "8: CHARMM27 
>> all-atom force field (CHARM22 plus CMAP for proteins) ". I wonder that 
>> whether the CHARMM27 all-atom force field here is equal to the CHARMM22/CMAP
>> 
>
>Well, not "equal" but it means that the "CHARMM27" files include C22/CMAP for 
>proteins.  There is no such thing as a CHARMM27 protein force field.  The C27 
>nucleic acid and lipid parameters came out at the same time as the C22/CMAP 
>protein force field, and got somewhat unfortunately lumped together in 
>nomenclature.
>
>-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.

[gmx-users] Question on force field

[YanhuaOuyang]

Hi, 
 I have run a protein MD simulation and choose a force field "8: CHARMM27 
all-atom force field (CHARM22 plus CMAP for proteins) ". I wonder that whether 
the CHARMM27 all-atom force field here is equal to the CHARMM22/CMAP

-- 
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] REMD analysis of trajectories

[YanhuaOuyang]

Do you mean  that the original trajectories REMD generated are belong to "one 
trajectory per temperature" (i.e. the md2.xtc is a trajectory at 298K)?



Ouyang




At 2017-06-01 21:00:52, "Mark Abraham" <mark.j.abra...@gmail.com> wrote:
>Hi,
>
>That's what you already have. See
>http://www.gromacs.org/Documentation/How-tos/REMD#Post-Processing
>
>Mark
>
>On Thu, Jun 1, 2017 at 5:37 AM YanhuaOuyang <15901283...@163.com> wrote:
>
>> Hi,
>>I have run a 100ns-REMD of protein, which has 20 replicas (i.e.
>> remd1.xtc, remd2.xtc, ..., remd20.xtc).  I want to analyze a trajectory at
>> specific temperature  such as a trajectory at experiment temperature 298K
>> rather than analyzing the continuous trajectory. I have known GROMACS
>> exchange coordinate when REMD running. Do I just analyze remd2.xtc of
>> replica 2(T=298K) if I want to analyze a trajectory at 298K? Do I need to
>> do something else on the trajectories to get a trajectory at specific
>> temperature(i.e. 298K)?
>>
>> Best regards,
>> Ouyang
>> --
>> 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.

[gmx-users] REMD analysis of trajectories

[YanhuaOuyang]

Hi,
   I have run a 100ns-REMD of protein, which has 20 replicas (i.e. remd1.xtc, 
remd2.xtc, ..., remd20.xtc).  I want to analyze a trajectory at specific 
temperature  such as a trajectory at experiment temperature 298K rather than 
analyzing the continuous trajectory. I have known GROMACS exchange coordinate 
when REMD running. Do I just analyze remd2.xtc of replica 2(T=298K) if I want 
to analyze a trajectory at 298K? Do I need to do something else on the 
trajectories to get a trajectory at specific temperature(i.e. 298K)?

Best regards,
Ouyang
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] failed to restart the REMD

[YanhuaOuyang]

Hi,
I have run REMD for 80ns. But I can't restart the REMD. The errors are as 
following:

Fatal error in MPI_Allreduce: Message truncated, error stack:
MPI_Allreduce(1339)...: MPI_Allreduce(sbuf=0x7fff4ac3fa90, 
rbuf=0x29af530, count=4, MPI_FLOAT, MPI_SUM, comm=0x8400) fai
led
MPIR_Allreduce_impl(1180).:
MPIR_Allreduce_intra(410).:
MPIR_Bcast_intra(1524): Failure during collective
MPIR_Bcast_intra(1499):
MPIR_Bcast_binomial(147)..:
MPIDI_CH3U_Receive_data_found(129): Message from rank 0 and tag 2 truncated; 
260 bytes received but buffer size is 16

I tried to restart the REMD many times and both use remd0.cpt and 
remd0_prev.cpt. But they all failed and appear error as above.
I don't know how to fix such problem.


Best regards,
Ouyang

-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] problem to restart the REMD

[YanhuaOuyang]

Hi,
I have run REMD for 80648ps. And I have to restart the REMD because of the 
limited time of super-computing center. However it always failed to restart 
from 80648ps. The errors are as following:

Fatal error in MPI_Allreduce: Message truncated, error stack:
MPI_Allreduce(1339)...: MPI_Allreduce(sbuf=0x7fff4ac3fa90, 
rbuf=0x29af530, count=4, MPI_FLOAT, MPI_SUM, comm=0x8400) fai
led
MPIR_Allreduce_impl(1180).:
MPIR_Allreduce_intra(410).:
MPIR_Bcast_intra(1524): Failure during collective
MPIR_Bcast_intra(1499):
MPIR_Bcast_binomial(147)..:
MPIDI_CH3U_Receive_data_found(129): Message from rank 0 and tag 2 truncated; 
260 bytes received but buffer size is 16

I tried to restart the REMD many times and both use remd0.cpt and 
remd0_prev.cpt. But they all failed and appear error as above.
I don't know how to solve the problem. I don't want to run from beginning since 
I have run such long time(80ns-REMD).
Does anyone know how fix such problem?


Best regards,
Ouyang
-- 
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] mdp options for REMD

[YanhuaOuyang]

Dear Mark,
Do you mean that both  "generate at 300K but themostat at 
500K"(gen-temp=300K,ref-t=500K) and "generate at 500K and thermostat at 
500K"(gen-temp=500K, ref-t=500K)  are OK?

And the latter one is recommended?

Ouyang








At 2017-03-20 21:56:35, "Mark Abraham" <mark.j.abra...@gmail.com> wrote:
>Hi,
>
>Will "generate at 300K but themostat at 500K" take more or less time to
>equilibrate than "generate at 500K and thermostat at 500K"? Both have the
>same desired end state when equilibration is over, so why not start closer
>to it?
>
>Mark
>
>On Mon, Mar 20, 2017 at 2:01 PM YanhuaOuyang <15901283...@163.com> wrote:
>
>> Hi,
>> I plan to run a REMD for a protein in explicit water. The temperature
>> is 300k-500k and there are 40 replicas.
>> I wander that are only the "ref-t" option in the equi_*.mdp files
>> different when equilibration stage ? what about gen-temp option. should I
>> make the gen-temp equal to ref-t (i.e. ref-t=gen-temp=500K)?
>>
>> Best regards,
>> Ouyang
>> --
>> 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.

[gmx-users] mdp options for REMD

[YanhuaOuyang]

Hi,
I plan to run a REMD for a protein in explicit water. The temperature is 
300k-500k and there are 40 replicas.
I wander that are only the "ref-t" option in the equi_*.mdp files different 
when equilibration stage ? what about gen-temp option. should I make the 
gen-temp equal to ref-t (i.e. ref-t=gen-temp=500K)?

Best regards,
Ouyang
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] gmx trjcat

[YanhuaOuyang]

Hi,
 I have a long trajectory , which is broken into 2 part because of disk 
space : traj 1  is 0ns-213ns, the other traj 2  is 200ns-300ns. How to 
concatenate this two trajectory into one single file trj 3(0ns-300ns) with 
trjcat since they have overlapping times(200ns-214ns)? how can I keep one of 
the overlapping time appropriately?

Best regards,
Ouyang.
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] demux.pl

[YanhuaOuyang]

Hi,
I have 60 replicas simulated with REMD using gromacs. I demultiplex .xtc files 
with demux.pl script. I know we can generate a continue coordinate trajectory 
using "gmx trjcat" combined with "-demux replica_index.xvg" option. However I 
am confused with using the option "-demux replica_temp.xvg"  to deal with .xtc 
files.
 What kind of trajectories we can get with "-demux replica_temp.xvg", are they 
coordinates at the same temperature?
Whats the difference between trajectories generated with "-demux 
replica_temp.xvg" and the original output trajectories?

Best regards,
Ouyang
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] high-temperature MD

[YanhuaOuyang]

Hi,
I want to perform a MD of an IDP, whose temperature is set to 380K. As we know, 
the MD is  equilibrated  firstly at NVT,  then at NPT ensemble and production 
MD at NPT ensemble normally.
Does someone know whether the 380K-MD  can only  perform at NVT ensemble since 
the temperature(380K) is a high temperature?
Should I run the MD(380K) at NPT ensemble or at NPT ensemble?


Best regards,
Ouyang
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] minimum distance between the protein and its mirror image

[YanhuaOuyang]

Hi,
   I am running a REMD of a disordered protein, I visualized the trajectory in 
VMD and I found that the protein is very close to the box edge.
   Then I use "gmx mindist " to  check  if a protein has seen its periodic 
image during simulation. When I used the command "gmx mindist -f remd_01.pdb -s 
remd.tpr -od mindist.xvg -pi" I choose the 1 group---protein. I choose some 
data from  mindist.xvg, they are as follow:
02.800  5.225  7.200  7.200  7.200
22.793  5.136  7.200  7.200  7.200
42.804  5.002  7.200  7.200  7.200
62.777  5.176  7.200  7.200  7.200
82.820  5.187  7.200  7.200  7.200
10   2.871  5.043  7.200  7.200  7.200
12   2.788  5.089  7.200  7.200  7.200
14   2.882  4.892  7.200  7.200  7.200
   
5154 4.153  3.415  7.200  7.200  7.200
5156 4.222  3.483  7.200  7.200  7.200
5158 4.154  3.608  7.200  7.200  7.200
5172 3.607  4.124  7.200  7.200  7.200
5174 3.556  4.140  7.200  7.200  7.200
5176 3.303  4.430  7.200  7.200  7.200
5178 3.291  4.297  7.200  7.200  7.200
...
5880 1.659  5.595  7.200  7.200  7.200
5882 1.787  5.564  7.200  7.200  7.200
5884 1.718  5.575  7.200  7.200  7.200
5886 1.669  5.654  7.200  7.200  7.200
5888 1.636  5.752  7.200  7.200  7.200
5890 1.590  5.761  7.200  7.200  7.200
5892 1.620  5.786  7.200  7.200  7.200
5894 1.513  5.791  7.200  7.200  7.200
5896 1.523  5.908  7.200  7.200  7.200
I set the short-range VDW and electrostatic cutoffs=1.0 nm, the distance 
between the outside of protein and the edge of box is 1.0 nm. the Minimum 
distance to periodic image ranges from 1.5 nm to 4.2 nm from the data above. 
While the deal value should be at least 2.0 nm, which is double the cutoff.
Do anyone knows the simulation is normal and if a protein has seen its periodic 
image during simulation?
which group should I choose when i using gmx mindist, protein, C-alpha or some 
else?

Best regards,
Ouyang
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] radius of gyration in REMD of protein

[YanhuaOuyang]

Hi,
   I am running a REMD of a protein,  which ranged from 270 to 500K in explicit 
water model with 60 replicas,  and I stop to analyse the REMD data after 
running for 50ns. I use the demux.pl script to get the continue the coordinate 
for each replica. Then I calculate the Rg value for each replica. However, the 
Rg fluctuation of each replica differs dramatically, some fluctuate 
dramatically, some converge well. Do someone knows the reason, or the 
fluctuation is normal ? How can I check my REMD is running correctlly?
the commad of Rg calculation is below:
gmx gyrate -s md_0_0.tpr   -f   *_continue_trajectory_pbc_mol.xtc  -o 
gyrate_*.xvg

Best regards,
Ouyang
-- 
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 the REMD

[YanhuaOuyang]

Dear Mark,
Sorry to disturb you again. What you mean is that the option “reseed 
-1” is used only once at the first start of REMD and I do not need to use it 
again for the forthcoming extended REMD simulation ? I wonder why?

> 在 2016年6月12日，下午10:53，Mark Abraham <mark.j.abra...@gmail.com> 写道：
> 
> Hi,
> 
> On Sun, Jun 12, 2016 at 3:22 PM YanhuaOuyang <15901283...@163.com> wrote:
> 
>> Dear Gromacs users,
>> 
>> I want to extend my REMD simulation to another 2 ns after a short REMD is
>> completed with Gromacs 5.0.2
>> 
>> my commands:
>> gmx convert-tpr -s previous.tpr -extend 2000 -o next.tpr
>> gmx mdrun -s next.tpr -cpi state.cpt -multi 30 -replex 1000 -reseed -1
>> 
>> I wonder if the option “-reseed -1” is needed again when extending the
>> REMD?
>> 
> 
> No
> 
> And how about the option: -e .edr, -c .gro, -g .log, are these options
>> necessary?
>> 
> 
> No.
> 
> Mark
> 
> 
>> Best regards,
>> Ouyang.
>> --
>> 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.

[gmx-users] Extending the REMD

[YanhuaOuyang]

Dear Gromacs users,

I want to extend my REMD simulation to another 2 ns after a short REMD is 
completed with Gromacs 5.0.2

my commands:
gmx convert-tpr -s previous.tpr -extend 2000 -o next.tpr
gmx mdrun -s next.tpr -cpi state.cpt -multi 30 -replex 1000 -reseed -1

I wonder if the option “-reseed -1” is needed again when extending the REMD? 
And how about the option: -e .edr, -c .gro, -g .log, are these options 
necessary?

Best regards,
Ouyang.
-- 
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] force filed parameters for phosphoserine with gromaces

[YanhuaOuyang]

What you mean is that I can use the AMBER parameters on the website 
(http://sites.pharmacy.manchester.ac.uk/bryce/amber 
<http://sites.pharmacy.manchester.ac.uk/bryce/amber>) and need to convert the 
format of the parameters to the one that GROMACS is compatible with in the .rtp 
entries? 
> 在 2016年6月3日，上午5:50，Justin Lemkul <jalem...@vt.edu> 写道：
> 
> 
> 
> On 6/2/16 10:55 AM, YanhuaOuyang wrote:
>> Dear Gromacs users,
>> 
>> I am going to run a MD of a 20-residue protein which is phosphorylated on the
>> Serine and Threonine residues with AMBER ff99SB-ILDN force field using
>> Gromacs5.0. When I run gmx pdb2gmx and choose AMBER ff99SB-ILDN force field,
>> it appears: fatal error: residues SEP not found in residue topology
>> database.
>> 
>> I search some papers, and they say that we need to add add force fields
>> parameters for the phosphorylated amino acids to the force filed parameter
>> files. But I do not know how to add force fields parameters for the
>> phosphorylated amino acids. Could anyone knows how to construct a model for
>> the phosphorylated protein?
>> 
> 
> AMBER parameters are already available:
> 
> http://sites.pharmacy.manchester.ac.uk/bryce/amber
> 
> You just need to convert the format and build suitable .rtp entries.  Or find 
> a force field that already has this done for you (CHARMM36, Gromos96 43a1p, 
> etc).
> 
> -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.

[gmx-users] force filed parameters for phosphoserine with gromaces

[YanhuaOuyang]

Dear Gromacs users,

I am going to run a MD of a 20-residue protein which is phosphorylated on the 
Serine and Threonine residues with AMBER ff99SB-ILDN force field using  
Gromacs5.0. When I run gmx pdb2gmx and choose AMBER ff99SB-ILDN force field, it 
appears:
fatal error: residues SEP not found in residue topology database.

I search some papers, and they say that we need to add add force fields 
parameters for the phosphorylated amino acids to the force filed parameter 
files. But I do not know how to add force fields parameters for the 
phosphorylated amino acids. Could anyone knows how to construct a model for the 
phosphorylated protein?

Best regards,
Ouyang.
-- 
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] Analyse REMD

[YanhuaOuyang]

tit=0
>}
>  }
>  if(printnextround){
>printit=1
>  }
>}
>  }' > $2
> }
> 
> 
> # Step 0: cleanup
> rm -f _ERROR_ problems* z* fixed.log*
> 
> 
> # Step 1: Find any problems
> # this tr command is necessary in case there was corruption in the .log file
> cat $LOG | tr -d '\0' > my.log
> find_problems my.log
> 
> # Step 2: Fix any problems
> n=0
> cp problems problems.$n
> cp problems.init problems.init.$n
> cp z z.$n
> 
> cat problems.0 | while read line; do
>  # exit the loop if there are no more problems
>  if (($(cat problems|wc -l)==0)); then
>break
>  fi
>  let "n++"
>  fn=($line)
>  fix_problems my.log fixed.log ${fn[0]} ${fn[1]} $STEP
>  cp fixed.log fixed.log.${n}
>  cp fixed.log my.log
>  find_problems fixed.log
>  cp problems problems.$n
>  cp problems.init problems.init.$n
>  cp z z.$n
> done
> 
> 
> # Want this file fixed.log to always exist so that I can use it in the DEMUX 
> scripts
> if [ ! -e fixed.log ]; then
>  mv my.log fixed.log
> else
>  rm my.log
> fi
> # Find any problems
> find_problems fixed.log
> 
> 
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
> <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of YanhuaOuyang 
> <15901283...@163.com>
> Sent: 22 May 2016 04:48:53
> To: gmx-us...@gromacs.org
> Subject: [gmx-users] Analyse REMD
> 
> Hi, I have run a REMD, which including 46 replicas. I searched how to analyze 
> my REMD statistics, but I am still confused how to analyze my result; how to 
> generate a continuous a energy distribution curve; how to deal with 46 .log 
> files. It seems so complicated.
> 
> one of my md.log file is as below:
> Replica exchange at step 998000 time 1996.0
> Repl 18 <-> 19  dE_term =  1.690e+01 (kT)
> Repl ex  01234 x  56 x  78 x  9   10   11   12   13   
> 14   15   16   17   18   19   20   21   22   23   24   25   26   27   28   29 
>   30   31   32   33   34   35   36   37   38   39   40   41   42   43   44   
> 45
> Repl pr   .01   .17   .03   1.0   1.0   .00   .00 
>   .01   .00   .00   .00   .00   .00   .00   .00   
> .00   .00   .00   .00   .00   .00   .00   .00
> 
> Replica exchange statistics
> Repl  499 attempts, 250 odd, 249 even
> Repl  average probabilities:
> Repl 0123456789   10   11   12   13   
> 14   15   16   17   18   19   20   21   22   23   24   25   26   27   28   29 
>   30   31   32   33   34   35   36   37   38   39   40   41   42   43   44   
> 45
> Repl  .07  .08  .05  .05  .06  .06  .06  .06  .06  .05  .05  .04  .03  
> .05  .03  .03  .03  .01  .03  .02  .04  .02  .02  .02  .01  .02  .02  .01  
> .01  .01  .01  .01  .01  .01  .01  .02  .01  .01  .02  .00  .02  .00  .02  
> .02  .01
> Repl  number of exchanges:
> Repl 0123456789   10   11   12   13   
> 14   15   16   17   18   19   20   21   22   23   24   25   26   27   28   29 
>   30   31   32   33   34   35   36   37   38   39   40   41   42   43   44   
> 45
> Repl   14   20   13   12   16   14   15   17   14   159   128   
> 13757256   1064625316 
>333234523424244
> 3
> Repl  average number of exchanges:
> Repl 0123456789   10   11   12   13   
> 14   15   16   17   18   19   20   21   22   23   24   25   26   27   28   29 
>   30   31   32   33   34   35   36   37   38   39   40   41   42   43   44   
> 45
> Repl  .06  .08  .05  .05  .06  .06  .06  .07  .06  .06  .04  .05  .03  
> .05  .03  .02  .03  .01  .02  .02  .04  .02  .02  .02  .01  .02  .01  .00  
> .02  .01  .01  .01  .01  .01  .02  .02  .01  .01  .02  .01  .02  .01  .02  
> .02  .01
> I wonder whether the result is ideal, do I need to optimize my temperature 
> distribution.
> 
> Best regards
> ouyang
> --
> 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.

[gmx-users] poor average exchange ratio for each replica

[YanhuaOuyang]

Dear Grimacs users,
I did use the equation:Ti=T0*ek*i  to generate a temperature distribution, 
after a 2-ns  REMD, I check the md.log file. I find the average exchange ratio 
for each replica is poor. the average exchange ratio is as below

Replica exchange statistics
Repl  499 attempts, 250 odd, 249 even
Repl  average probabilities:
Repl 0123456789   10   11   12   13   
14   15   16   17   18   19   20   21   22   23   24   25   26   27   28   29   
30   31   32   33   34   35   36   37   38   39   40   41   42   43   44   45
Repl  .07  .08  .05  .05  .06  .06  .06  .06  .06  .05  .05  .04  .03  .05  
.03  .03  .03  .01  .03  .02  .04  .02  .02  .02  .01  .02  .02  .01  .01  .01  
.01  .01  .01  .01  .01  .02  .01  .01  .02  .00  .02  .00  .02  .02  .01

Repl  number of exchanges:
Repl 0123456789   10   11   12   13   
14   15   16   17   18   19   20   21   22   23   24   25   26   27   28   29   
30   31   32   33   34   35   36   37   38   39   40   41   42   43   44   45
Repl   14   20   13   12   16   14   15   17   14   159   128   13  
  757256   10646253163  
  332345234242443

 the temperature distribution: 270.00 272.84 275.77 278.79 281.91 285.12 288.43 
291.84 295.36 299.00 302.75 306.61 310.60 314.72 318.97 323.36 327.89 332.56 
337.39 342.38 347.52 352.83 358.32 363.98 369.82 375.86 382.09 388.51 395.15 
401.99 409.05 416.33 423.84 431.59 439.58 447.81 456.29 465.04 474.05 483.34 
492.92 502.78 512.96 523.45 534.28 545.46.

the temperature is reasonable, but the acceptance ratio is far from 0.2-0.3. So 
I get a another temperature distribution with the 
website:http://origami.phys.rpi.edu/racc/rate_of_acceptance.php 
  ,the average 
exchange ratio still is  less than 0.05. 
I really do not know how to improve the situation. What should I do in the next 
step? How should I improve such a low exchange ratio?

best regards,
Ouyang



-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] Analyse REMD

[YanhuaOuyang]

Hi, I have run a REMD, which including 46 replicas. I searched how to analyze 
my REMD statistics, but I am still confused how to analyze my result; how to 
generate a continuous a energy distribution curve; how to deal with 46 .log 
files. It seems so complicated.

one of my md.log file is as below:
Replica exchange at step 998000 time 1996.0
Repl 18 <-> 19  dE_term =  1.690e+01 (kT)
Repl ex  01234 x  56 x  78 x  9   10   11   12   13   
14   15   16   17   18   19   20   21   22   23   24   25   26   27   28   29   
30   31   32   33   34   35   36   37   38   39   40   41   42   43   44   45
Repl pr   .01   .17   .03   1.0   1.0   .00   .00   
.01   .00   .00   .00   .00   .00   .00   .00   
.00   .00   .00   .00   .00   .00   .00   .00

Replica exchange statistics
Repl  499 attempts, 250 odd, 249 even
Repl  average probabilities:
Repl 0123456789   10   11   12   13   
14   15   16   17   18   19   20   21   22   23   24   25   26   27   28   29   
30   31   32   33   34   35   36   37   38   39   40   41   42   43   44   45
Repl  .07  .08  .05  .05  .06  .06  .06  .06  .06  .05  .05  .04  .03  .05  
.03  .03  .03  .01  .03  .02  .04  .02  .02  .02  .01  .02  .02  .01  .01  .01  
.01  .01  .01  .01  .01  .02  .01  .01  .02  .00  .02  .00  .02  .02  .01
Repl  number of exchanges:
Repl 0123456789   10   11   12   13   
14   15   16   17   18   19   20   21   22   23   24   25   26   27   28   29   
30   31   32   33   34   35   36   37   38   39   40   41   42   43   44   45
Repl   14   20   13   12   16   14   15   17   14   159   128   13  
  757256   10646253163  
  332345234242443
Repl  average number of exchanges:
Repl 0123456789   10   11   12   13   
14   15   16   17   18   19   20   21   22   23   24   25   26   27   28   29   
30   31   32   33   34   35   36   37   38   39   40   41   42   43   44   45
Repl  .06  .08  .05  .05  .06  .06  .06  .07  .06  .06  .04  .05  .03  .05  
.03  .02  .03  .01  .02  .02  .04  .02  .02  .02  .01  .02  .01  .00  .02  .01  
.01  .01  .01  .01  .02  .02  .01  .01  .02  .01  .02  .01  .02  .02  .01
 I wonder whether the result is ideal, do I need to optimize my temperature 
distribution.

Best regards
ouyang
-- 
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] REMD error

[YanhuaOuyang]

Hi,
I have installed the openmpi 1.10, and I can run mpirun. When I installed 
grimaces 5.1, I configured -DGMX_MPI=on.
And the error still happens .
> 在 2016年5月13日，下午3:59，Mark Abraham <mark.j.abra...@gmail.com> 写道：
> 
> Hi,
> 
> Yes. Exactly as the error message says, you need to compile GROMACS
> differently, with real MPI support. See
> http://manual.gromacs.org/documentation/5.1.2/user-guide/mdrun-features.html#running-multi-simulations
> 
> Mark
> 
> On Fri, May 13, 2016 at 9:47 AM YanhuaOuyang <15901283...@163.com> wrote:
> 
>> Hi,
>> I am running a REMD of a protein, when I submit "gmx mdrun -s
>> md_0_${i}.tpr -multi 46 -replex 1000 -reseed -1", it fails as the below
>> Fatal error:
>> mdrun -multi or -multidir are not supported with the thread-MPI library.
>> Please compile GROMACS with a proper external MPI library.
>> I have installed the openmpi  and gromacs 5.1.
>> Do anyone know the problem.
>> 
>> yours sincerelly,
>> Ouyang
>> --
>> 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.

[gmx-users] REMD error

[YanhuaOuyang]

Hi,
I am running a REMD of a protein, when I submit "gmx mdrun -s md_0_${i}.tpr 
-multi 46 -replex 1000 -reseed -1", it fails as the below
Fatal error:
mdrun -multi or -multidir are not supported with the thread-MPI library. Please 
compile GROMACS with a proper external MPI library.
I have installed the openmpi  and gromacs 5.1.
Do anyone know the problem.

yours sincerelly,
Ouyang
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] REMD on more than one node

[YanhuaOuyang]

Hi,
I am running a REMD with grimacs 5.0, I have 46 replica, 4 nodes, 16 cores per 
node. how can I use my compute resource and what’s the command of “gmx mdrun”?
the command is below, I am not sure weather it is right
mpirun -np 4 -npme gmx mdrun -s md_01.tpr  -multi 46 -replex 500 -reseed -1.
mpirun -np 4 -npme gmx mdrun -s md_02.tpr  -multi 46 -replex 500 -reseed -1.
mpirun -np 4 -npme gmx mdrun -s md_03.tpr  -multi 46 -replex 500 -reseed -1.
…
mpirun -np 4 -npme gmx mdrun -s md_46.tpr  -multi 46 -replex 500 -reseed -1.


-- 
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] REMD--how to determine the temperature distribution

[YanhuaOuyang]

When I choose NVT, it appear like this: "ERROR: Can not do constant volume 
yet!”, do you have other ways to determine the temperature except the two 
websites?
> 在 2016年4月26日，下午8:16，Mark Abraham <mark.j.abra...@gmail.com> 写道：
> 
> No, just choose NVT.
> 
> Mark
> 
> On Tue, 26 Apr 2016 13:42 YanhuaOuyang <15901283...@163.com> wrote:
> 
>> Thank you so much, but the latter one is only suitable for REMD in NPT
>> ensemble.
>>> 在 2016年4月26日，上午1:20，Christopher Neale <chris.ne...@alum.utoronto.ca> 写道：
>>> 
>>> There are many published approaches. Here is the one that I use:
>> http://origami.phys.rpi.edu/racc/rate_of_acceptance.php
>>> Another example is here: http://folding.bmc.uu.se/remd/
>>> 
>>> 
>>> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
>> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of
>> YanhuaOuyang <15901283...@163.com>
>>> Sent: 25 April 2016 10:36
>>> To: gmx-us...@gromacs.org
>>> Subject: [gmx-users] REMD--how to determine the temperature distribution
>>> 
>>> Dear all,
>>>   I am going to run a REMD of a protein(explicit solvent) in NVT
>> ensemble with gromacs, but I have trouble in determining a optimum
>> temperature  distribution.Can anybody know the ways to determine the
>> temperature?
>>> --
>>> 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.
> -- 
> 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] REMD--how to determine the temperature distribution

[YanhuaOuyang]

Thank you so much, but the latter one is only suitable for REMD in NPT ensemble.
> 在 2016年4月26日，上午1:20，Christopher Neale <chris.ne...@alum.utoronto.ca> 写道：
> 
> There are many published approaches. Here is the one that I use: 
> http://origami.phys.rpi.edu/racc/rate_of_acceptance.php
> Another example is here: http://folding.bmc.uu.se/remd/
> 
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
> <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of YanhuaOuyang 
> <15901283...@163.com>
> Sent: 25 April 2016 10:36
> To: gmx-us...@gromacs.org
> Subject: [gmx-users] REMD--how to determine the temperature distribution
> 
> Dear all,
>I am going to run a REMD of a protein(explicit solvent) in NVT 
> ensemble with gromacs, but I have trouble in determining a optimum 
> temperature  distribution.Can anybody know the ways to determine the 
> temperature?
> --
> 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.

[gmx-users] REMD--how to determine the temperature distribution

[YanhuaOuyang]

Dear all,
I am going to run a REMD of a protein(explicit solvent) in NVT ensemble 
with gromacs, but I have trouble in determining a optimum temperature  
distribution.Can anybody know the ways to determine the temperature?
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] REMD of IDPs

[YanhuaOuyang]

Hi, I have a sequence of an intrinsically disordered protein, I have no idea 
how to start my REMD with gromacs. e.g. how to convert my sequence into a pdb 
file
-- 
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.