Re: [gmx-users] How to deal with unexpected reactions in umbrella sampling?

[Qing Lv]

Thank you, Quyen. I will look into this paper.


Qing





At 2020-02-20 18:45:58, "Quyen V. Vu"  wrote:
>Hi,
>you can think about employed multi-dimensional umbrella sampling and used
>3D-WHAM to derived the PMF as professor Pander did in this paper: Petrone,
>P. M., Snow, C. D., Lucent, D., & Pande, V. S. (2008). Side-chain
>recognition and gating in the ribosome exit tunnel. *Proceedings of the
>National Academy of Sciences of the United States of America*, *105*(43),
>16549–16554. https://doi.org/10.1073/pnas.0801795105
>
>I don't know whether he delivered the code for 3D-WHAM or not
>
>Best,
>
>On Thu, Feb 20, 2020 at 2:58 AM Qing Lv  wrote:
>
>> Dear Colleagues,
>>
>>
>> I am doing an umbrella sampling of an enzymatic reaction using QM/MM.
>> However, as the reaction coordinate exceeds a certain value, an unexpected
>> reaction, which is obviously unreasonable, often occurs during the umbrella
>> sampling. So, how to deal with such problem? The only method I can think is
>> to impose additional restraints to avoid this reaction, but the additional
>> restraints will probably affect the umbrella sampling (although the
>> additional restraints are not related to the reaction coordinate).
>>
>>
>> Thanks,
>> Qing
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[gmx-users] How to deal with unexpected reactions in umbrella sampling?

[Qing Lv]

Dear Colleagues,


I am doing an umbrella sampling of an enzymatic reaction using QM/MM. However, 
as the reaction coordinate exceeds a certain value, an unexpected reaction, 
which is obviously unreasonable, often occurs during the umbrella sampling. So, 
how to deal with such problem? The only method I can think is to impose 
additional restraints to avoid this reaction, but the additional restraints 
will probably affect the umbrella sampling (although the additional restraints 
are not related to the reaction coordinate).


Thanks,
Qing
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Re: [gmx-users] Error bar for umbrella sampling?

[Qing Lv]

Thank you Alexander and Quyen. I will try these tools.


Qing





At 2020-01-14 01:01:31, "Александр Лашков"  wrote:
>In pymbar package error estimate directly. Example usage this package for
>umbrella sampling can be  found on github page for this package
>Alexander
>
>пн, 13 янв. 2020 г., 17:35 Qing Lv :
>
>> Dear All,
>>
>>
>> I wonder if the error bars are necessary for umbrella sampling in PMF
>> calculation? If yes, how should the error bars be calculated? Need I do 2~3
>> repeats (with different random initial velocites assigned)?
>>
>>
>> Thanks,
>> Qing
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[gmx-users] Error bar for umbrella sampling?

[Qing Lv]

Dear All,


I wonder if the error bars are necessary for umbrella sampling in PMF 
calculation? If yes, how should the error bars be calculated? Need I do 2~3 
repeats (with different random initial velocites assigned)?


Thanks,
Qing
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Re: [gmx-users] Is minimization and equilibration needed for umbrella sampling?

[Qing Lv]

Thank you, Justin. I start each run by randomly generate velocities at 300K, 
and each run is quite stable. So, is it appropriate to regard the first 20 ps 
(this is a QM/MM MD) of each run as the equilibration and just discard this 20 
ps in the final wham analysis?


Best,
Qing



At 2020-01-13 21:29:23, "Justin Lemkul"  wrote:
>
>
>On 1/10/20 11:02 AM, Qing Lv wrote:
>> Dear Colleagues,
>>
>>
>> I am doing a QM/MM umbrella sampling to calculate the PMF of an enzymatic 
>> reaction. The initial coordinates (with solvents and ions) for each sampling 
>> window were extracted from previous trajectories. The reaction coordinate 
>> (bond length difference) of each initial frame was closed to the center of 
>> the window. So, need I do energy-minimization and equilibration for each 
>> window? Since each initial conformation has no bad clashes (actually they 
>> can run MD well without minimizations) and is closed to the window center, I 
>> cannot understand why minimization and equilibration are still needed (as a 
>> lot of references do so).
>
>I don't think minimization is essential, but unless you saved the full 
>state (including velocities) for each snapshot, then you need to 
>re-equilibrate. Otherwise you're either starting from T=0 K (gen-vel=no) 
>or a random state that is not necessarily stable (gen-vel=yes).
>
>-Justin
>
>-- 
>==
>
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>
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[gmx-users] Is minimization and equilibration needed for umbrella sampling?

[Qing Lv]

Dear Colleagues,


I am doing a QM/MM umbrella sampling to calculate the PMF of an enzymatic 
reaction. The initial coordinates (with solvents and ions) for each sampling 
window were extracted from previous trajectories. The reaction coordinate (bond 
length difference) of each initial frame was closed to the center of the 
window. So, need I do energy-minimization and equilibration for each window? 
Since each initial conformation has no bad clashes (actually they can run MD 
well without minimizations) and is closed to the window center, I cannot 
understand why minimization and equilibration are still needed (as a lot of 
references do so).


Thanks,
Qing
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Re: [gmx-users] File forcefield.itp, line 4 Last line read: '[ defaults ]' Invalid order for directive defaults

[Qing Lv]

The problem has been solved. I forgot to delete some entries when using .top 
file as .itp file.


Thanks,
Qing


At 2017-06-23 15:36:32, "Mark Abraham" <mark.j.abra...@gmail.com> wrote:
>Hi,
>
>You can't just paste together two topology files intended to stand alone
>e.g. because they have [defaults] sections. You can #include files, but
>they have to follow the structure of the example in chapter 5 of the manual
>(and every tutorial). Defaults, then atomtypes and parameters, then
>moleculetypes, then system.
>
>Mark
>
>On Fri, Jun 23, 2017 at 5:47 AM Qing Lv <lvqingjie...@163.com> wrote:
>
>> I changed the order of .itp file and put the "topol_ATP.itp" ahead of
>> protein.itp . However, I got the following errors this time:
>> Fatal error:
>> Syntax error - File forcefield.itp, line 6
>> Last line read:
>> '  11   no  1.0 1.0'
>> Found a second defaults directive.
>>
>>
>> P.S.
>> My topology file includes ATP, Protein, and Mg2+.  I tried to remove Mg2+
>> (probably inappropriate) but still got the same errors.
>>
>>
>> Thanks,
>> Qing
>>
>>
>>
>> At 2017-06-23 09:46:49, "Qing Lv" <lvqingjie...@163.com> wrote:
>> >Dear All,
>> >
>> >
>> >I am setting up a simulation of protein-ATP complex. I manually combined
>> the coordinates and topologies of the protein and ATP together, and ran
>> editconf and solvate successfully. However, when I ran grompp, errors
>> occurred:
>> >Syntax error - File forcefield.itp, line 4
>> >Last line read:
>> >'[ defaults ]'
>> >Invalid order for directive defaults
>> >
>> >
>> >I checked the .itp files I used and did not find "[ defaults ]" pattern.
>> How to fix it?
>> >Thanks,
>> >Qing
>> >--
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Re: [gmx-users] 5-letter atom names in topology files

[Qing Lv]

At 2017-06-23 21:55:39, "Justin Lemkul" <jalem...@vt.edu> wrote:
>
>
>On 6/23/17 9:53 AM, Qing Lv wrote:
>> I tried pdb2gmx -merge interactive or -chainsep interactive, but neither 
>> work...
>
>There is no chain information in a .gro so this approach cannot work.  If you 
>have a multimeric complex, and you need to use these weird 5-character names, 
>process each .gro separately and merge the topologies manually (convert .top 
>-> 
>.itp and list them as #include statements in a new .top).



This is just what I have tried and succeeded eventually... Previously I made 
some mistakes when converting .top files to .itp.
Thanks.
Qing


>
>Or:
>
>1. Use a different force field that doesn't require format-breaking atom names.
>2. Change the names in the .rtp and coordinate file to preserve format 
>standards.
>
>-Justin
>
>-- 
>==
>
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>
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Re: [gmx-users] 5-letter atom names in topology files

[Qing Lv]

I tried pdb2gmx -merge interactive or -chainsep interactive, but neither work...
Qing


At 2017-06-23 17:19:55, "Fitsiou, Eleni"  wrote:
>Hi ,
>Rename your chains and you could use   -merge interactive and  the -ter flag
>Best 
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Re: [gmx-users] 5-letter atom names in topology files

[Qing Lv]

My protein contains 2 chains, and ILE294 is the C-terminus of chain 1. When I 
used pdb2gmx to process the GRO file, it can recognize N-terminus of chain 1 
and C-terminus of chain 2, but cannot recognize C-terminus of chain 1. Since 
there is no chain separators in GRO files (like "TER" in PDB), pdb2gmx might 
regard all aminoacids as one single chain.
Sorry for not having explained clearly in previous emails. Any suggestions?


Many thanks,
Qing


At 2017-06-23 16:24:13, "Qing Lv" <lvqingjie...@163.com> wrote:
>Dear Mark,
>
>
>Actually I had tried the method you suggested, but got such errors (pdb2gmx):
>Fatal error:
>Atom O1 in residue ILE 294 was not found in rtp entry ILE with 9 atoms while 
>sorting atoms.
>ILE294 is C-terminus of my protein. I looked up in aminoacids.rtp and there 
>are no atom "O1" or "O2" in ILE entry; however, I never got such errors when 
>using pdb2gmx to process PDB files. Maybe, pdb2gmx can only process terminal 
>residues for PDB files?
>
>
>Also, I have tried to process protein and ATP separately with pdb2gmx and then 
>combined them together, but met problems. That's why I sent another 2 emails...
>
>
>Qing
>
>
>At 2017-06-23 15:33:17, "Mark Abraham" <mark.j.abra...@gmail.com> wrote:
>>Hi,
>>
>>I suggest you produce your initial conformation in .gro format, which
>>permits five-character atom names. That might mean using editconf on your
>>.pdb file, and then manually renaming atoms.
>>
>>Mark
>>
>>On Fri, Jun 23, 2017 at 3:55 AM Qing Lv <lvqingjie...@163.com> wrote:
>>
>>> Hi,
>>>
>>>
>>> Gromos 54a7 force field has built-in topologies for some small molecules,
>>> like ATP. In these topologies, many atoms have names of up to 5 letters,
>>> such as AO1PA and AO2PB. However, PDB files seem do not support 5-letter
>>> atom names. So, if I name an atom "AO2PB" in PDB, it will be truncated to
>>> "AO2P" or "O2PB" when executing pdb2gmx, and these atoms cannot be
>>> recognized then.
>>> Anyone know how to solvate this problem? Many thanks ^_^
>>>
>>>
>>> Qing
>>> --
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>>>
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Re: [gmx-users] 5-letter atom names in topology files

[Qing Lv]

Dear Mark,


Actually I had tried the method you suggested, but got such errors (pdb2gmx):
Fatal error:
Atom O1 in residue ILE 294 was not found in rtp entry ILE with 9 atoms while 
sorting atoms.
ILE294 is C-terminus of my protein. I looked up in aminoacids.rtp and there are 
no atom "O1" or "O2" in ILE entry; however, I never got such errors when using 
pdb2gmx to process PDB files. Maybe, pdb2gmx can only process terminal residues 
for PDB files?


Also, I have tried to process protein and ATP separately with pdb2gmx and then 
combined them together, but met problems. That's why I sent another 2 emails...


Qing


At 2017-06-23 15:33:17, "Mark Abraham" <mark.j.abra...@gmail.com> wrote:
>Hi,
>
>I suggest you produce your initial conformation in .gro format, which
>permits five-character atom names. That might mean using editconf on your
>.pdb file, and then manually renaming atoms.
>
>Mark
>
>On Fri, Jun 23, 2017 at 3:55 AM Qing Lv <lvqingjie...@163.com> wrote:
>
>> Hi,
>>
>>
>> Gromos 54a7 force field has built-in topologies for some small molecules,
>> like ATP. In these topologies, many atoms have names of up to 5 letters,
>> such as AO1PA and AO2PB. However, PDB files seem do not support 5-letter
>> atom names. So, if I name an atom "AO2PB" in PDB, it will be truncated to
>> "AO2P" or "O2PB" when executing pdb2gmx, and these atoms cannot be
>> recognized then.
>> Anyone know how to solvate this problem? Many thanks ^_^
>>
>>
>> Qing
>> --
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Re: [gmx-users] File forcefield.itp, line 4 Last line read: '[ defaults ]' Invalid order for directive defaults

[Qing Lv]

I changed the order of .itp file and put the "topol_ATP.itp" ahead of 
protein.itp . However, I got the following errors this time:
Fatal error:
Syntax error - File forcefield.itp, line 6
Last line read:
'  11   no  1.0 1.0'
Found a second defaults directive.


P.S.
My topology file includes ATP, Protein, and Mg2+.  I tried to remove Mg2+ 
(probably inappropriate) but still got the same errors.


Thanks,
Qing



At 2017-06-23 09:46:49, "Qing Lv" <lvqingjie...@163.com> wrote:
>Dear All,
>
>
>I am setting up a simulation of protein-ATP complex. I manually combined the 
>coordinates and topologies of the protein and ATP together, and ran editconf 
>and solvate successfully. However, when I ran grompp, errors occurred:
>Syntax error - File forcefield.itp, line 4
>Last line read:
>'[ defaults ]'
>Invalid order for directive defaults
>
>
>I checked the .itp files I used and did not find "[ defaults ]" pattern. How 
>to fix it?
>Thanks,
>Qing
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[gmx-users] 5-letter atom names in topology files

[Qing Lv]

Hi,


Gromos 54a7 force field has built-in topologies for some small molecules, like 
ATP. In these topologies, many atoms have names of up to 5 letters, such as 
AO1PA and AO2PB. However, PDB files seem do not support 5-letter atom names. 
So, if I name an atom "AO2PB" in PDB, it will be truncated to "AO2P" or "O2PB" 
when executing pdb2gmx, and these atoms cannot be recognized then.
Anyone know how to solvate this problem? Many thanks ^_^


Qing
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[gmx-users] File forcefield.itp, line 4 Last line read: '[ defaults ]' Invalid order for directive defaults

[Qing Lv]

Dear All,


I am setting up a simulation of protein-ATP complex. I manually combined the 
coordinates and topologies of the protein and ATP together, and ran editconf 
and solvate successfully. However, when I ran grompp, errors occurred:
Syntax error - File forcefield.itp, line 4
Last line read:
'[ defaults ]'
Invalid order for directive defaults


I checked the .itp files I used and did not find "[ defaults ]" pattern. How to 
fix it?
Thanks,
Qing
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Re: [gmx-users] How to read .dat file

[Qing Lv]

The file rms.xvg contains only RMSD values against the reference PDB structure; 
what I need to know is the contents of RMSD matrix between 2 trajectories.


Qing


At 2017-06-15 15:17:08, "Dd H" <ddhe...@gmail.com> wrote:
>I think this link should be helpful.
>http://manual.gromacs.org/programs/gmx-rms.html
>You can have a look at rms.xvg file, it contains rmsd values.
>
>Best regards,
>Dading Huang
>
>
>On Wed, Jun 14, 2017 at 7:05 PM, Qing Lv <lvqingjie...@163.com> wrote:
>
>> I generated a .dat file with the following command:
>> gmx rms -s .pdb -f 1.xtc -f2 2.xtc -n index.ndx -o rms.xvg -m rms.xpm
>> -bin rms.dat
>> But how to read the binary file rms.dat?
>>
>>
>> The reason is that,
>> I found the lowest RMSD in RMSD matrix (rms.xpm) is 0.52 nm; how to know
>> which frame in 1.xtc and which frame in 2.xtc have this minimal RMSD?
>>
>>
>> Thanks,
>> Qing
>> --
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[gmx-users] How to read .dat file

[Qing Lv]

I generated a .dat file with the following command:
gmx rms -s .pdb -f 1.xtc -f2 2.xtc -n index.ndx -o rms.xvg -m rms.xpm -bin 
rms.dat
But how to read the binary file rms.dat?


The reason is that,
I found the lowest RMSD in RMSD matrix (rms.xpm) is 0.52 nm; how to know which 
frame in 1.xtc and which frame in 2.xtc have this minimal RMSD?


Thanks,
Qing
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Re: [gmx-users] Anyone use FMA (Functional Mode Analysis) ?

[Qing Lv]

Thank you. I have just received the response from Dr. Jochen Hub and solved 
this problem.Qing

At 2017-05-14 22:42:30, "Qing Lv" <lvqingjie...@163.com> wrote:
>Hi Colleagues,
>
>I am trying to compile FMA (Functional Mode Analysis), developed by Dr. Jochen 
>Hub. However, I met difficulties in the installation. According to the 
>instructions, I installed Gromacs 4.0.5 (also tried 4.0.7) and the related 
>libraries (libf2c, lapack, mpich, etc).
>Firstly, cmake . did not give error messages;
>When executing make, I got the following messages:
>[ 80%] Building C object 
>CMakeFiles/fma.dir/files/gromacs-4.0.5/src/tools/eigensolver.c.o
>/files/gromacs-4.0.5/src/tools/eigensolver.c: In function ‘eigensolver’:
>/files/gromacs-4.0.5/src/tools/eigensolver.c:65: warning: unused variable ‘iu’
>/files/gromacs-4.0.5/src/tools/eigensolver.c:65: warning: unused variable ‘il’
>Linking C executable fma
>/usr/bin/ld: cannot find -lmd_mpi
>collect2: ld returned 1 exit status
>make[2]: *** [fma] Error 1
>make[1]: *** [CMakeFiles/fma.dir/all] Error 2
>make: *** [all] Error 2
>
>
>I googled this message but have not found useful info. Also, it seems that Dr. 
>Hub might have stopped the maintenance of this program.
>It seems that "-lmd_mpi" is a component of Gromacs. I tried higher GMX 
>versions like 4.5.4, but found it incompatible with FMA. Have anyone used this 
>program? Any help is highly appreciated.
>
>
>Thanks a lot.
>Qing
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[gmx-users] Anyone use FMA (Functional Mode Analysis) ?

[Qing Lv]

Hi Colleagues,

I am trying to compile FMA (Functional Mode Analysis), developed by Dr. Jochen 
Hub. However, I met difficulties in the installation. According to the 
instructions, I installed Gromacs 4.0.5 (also tried 4.0.7) and the related 
libraries (libf2c, lapack, mpich, etc).
Firstly, cmake . did not give error messages;
When executing make, I got the following messages:
[ 80%] Building C object 
CMakeFiles/fma.dir/files/gromacs-4.0.5/src/tools/eigensolver.c.o
/files/gromacs-4.0.5/src/tools/eigensolver.c: In function ‘eigensolver’:
/files/gromacs-4.0.5/src/tools/eigensolver.c:65: warning: unused variable ‘iu’
/files/gromacs-4.0.5/src/tools/eigensolver.c:65: warning: unused variable ‘il’
Linking C executable fma
/usr/bin/ld: cannot find -lmd_mpi
collect2: ld returned 1 exit status
make[2]: *** [fma] Error 1
make[1]: *** [CMakeFiles/fma.dir/all] Error 2
make: *** [all] Error 2


I googled this message but have not found useful info. Also, it seems that Dr. 
Hub might have stopped the maintenance of this program.
It seems that "-lmd_mpi" is a component of Gromacs. I tried higher GMX versions 
like 4.5.4, but found it incompatible with FMA. Have anyone used this program? 
Any help is highly appreciated.


Thanks a lot.
Qing
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[gmx-users] Interactive Essential Dynamics (IED) installation: vmdnumpy module not available

[Qing Lv]

Dear all,


I am trying to compile IED (Interactive essential dynamics) according to the 
instructions of
http://mccammon.ucsd.edu/ied/
However, I always got such errors:
--
vmd > gopython
Info) Starting Python...
Traceback (most recent call last):
  File "", line 1, in 
ValueError: vmdnumpy module not available.
Info) Text interpreter now Python
Traceback (most recent call last):
  File "", line 1, in 
  File "/usr/local/lib/vmd1.8.7/vmd/scripts/python/Tkinter.py", line 59, in 

import _tkinter # If this fails your Python may not be configured for Tk
ImportError: No module named _tkinter
>>> import vmdnumpy,Numeric
Traceback (most recent call last):
  File "VMD", line 1, in 
ImportError: No module named vmdnumpy
>>> 
---
I have tried Python 2.5, 2.6, and 2.7, and VMD version from 1.8.4 to 1.9.3. The 
installation of Python Numeric Version 24.2 is successful.


Anyone have successfully compiled IED? Thanks a lot


Best wishes,
Qing
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Re: [gmx-users] How to write pull code in umbrella sampling

[Qing Lv]

Thank you so much, Justin. I will look into PLUMED.


Qing


At 2017-04-08 19:05:28, "Justin Lemkul" <jalem...@vt.edu> wrote:
>
>
>On 4/8/17 1:46 AM, Qing Lv wrote:
>> Thank you, Justin.
>>
>>
>> My goal is to investigate the conformation transition of a 30aa loop between 
>> an unstructured loop and an alpha-helix. I found a transition pathway on 
>> free energy landscape and selected a number of frames along the pathway for 
>> umbrella sampling. So, should I define C-alpha of this 30aa loop as 
>> pull-group1 and C-alpha of the remaining part as pull-group2 ? Would the 
>> pull geometry still be "distance"? But this will just restrain the distance 
>> between COM of the 2 groups to the initial distance, but cannot restrain the 
>> conformation of the loop.
>> Or need I divide the loop into many small segments (pull-groups) and define 
>> the pull coordinates separately? This seems horrible...
>>
>
>You should probably be looking at a more advanced, multi-dimensional bias or 
>collective variable.  Look into PLUMED.  GROMACS is going to be limited to a 
>linear reaction coordinate, which may not capture everything you need in such 
>a 
>large transition.
>
>-Justin
>
>>
>> Thanks,
>> Qing
>>
>>
>> At 2017-04-08 09:06:46, "Justin Lemkul" <jalem...@vt.edu> wrote:
>>>
>>>
>>> On 4/7/17 8:56 PM, Qing Lv wrote:
>>>> Dear Colleagues,
>>>>
>>>>
>>>> I am trying to do an umbrella sampling using a series of conformations 
>>>> extracted from several unbiased MD trajectories. But I am not sure about 
>>>> the pull code in .mdp file.
>>>> Below is the pull code from the tutorial of Dr. Justin Lemkul :
>>>> define  = -DPOSRES_B ; (Why ??)
>>>
>>> Did you read the paper I linked from the tutorial, which explains why this 
>>> is
>>> done for this very specific case?
>>>
>>>> ; Pull code
>>>> pull= yes
>>>> pull_ngroups= 2
>>>> pull_ncoords= 1
>>>> pull_group1_name= Chain_B
>>>> pull_group2_name= Chain_A
>>>> pull_coord1_type= umbrella  ; harmonic biasing force
>>>> pull_coord1_geometry= distance  ; simple distance increase
>>>> pull_coord1_groups  = 1 2
>>>> pull_coord1_dim = N N Y
>>>> pull_coord1_rate= 0.0
>>>> pull_coord1_k   = 1000  ; kJ mol^-1 nm^-2
>>>> pull_coord1_start   = yes   ; define initial COM distance > 0
>>>>
>>>>
>>>>
>>>> Conformations in Justin's tutorial are from steered MD. However, my 
>>>> conformations are not from SMD, and I have not done SMD on this system. 
>>>> So, how to define pull_group1 and pull_group2? And pull_coord1_geometry 
>>>> still set to "distance" ?
>>>
>>> The pull groups don't depend on where the configurations came from.  They 
>>> define
>>> the reaction coordinate.  You can use whatever pull geometry makes sense; 
>>> in the
>>> tutorial it is a simple linear reaction coordinate directly along the 
>>> z-axis.
>>> Other applications may require different definitions.
>>>
>>>> Also, need I fix any part of protein in umbrella sampling (with " -DPOSRES 
>>>> ") ? Why?
>>>
>>> Generally, no, but you haven't given any useful detail about what your
>>> simulation system is.
>>>
>>> -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 reques

Re: [gmx-users] How to write pull code in umbrella sampling

[Qing Lv]

Thank you, Justin.


My goal is to investigate the conformation transition of a 30aa loop between an 
unstructured loop and an alpha-helix. I found a transition pathway on free 
energy landscape and selected a number of frames along the pathway for umbrella 
sampling. So, should I define C-alpha of this 30aa loop as pull-group1 and 
C-alpha of the remaining part as pull-group2 ? Would the pull geometry still be 
"distance"? But this will just restrain the distance between COM of the 2 
groups to the initial distance, but cannot restrain the conformation of the 
loop.
Or need I divide the loop into many small segments (pull-groups) and define the 
pull coordinates separately? This seems horrible...


Thanks,
Qing


At 2017-04-08 09:06:46, "Justin Lemkul" <jalem...@vt.edu> wrote:
>
>
>On 4/7/17 8:56 PM, Qing Lv wrote:
>> Dear Colleagues,
>>
>>
>> I am trying to do an umbrella sampling using a series of conformations 
>> extracted from several unbiased MD trajectories. But I am not sure about the 
>> pull code in .mdp file.
>> Below is the pull code from the tutorial of Dr. Justin Lemkul :
>> define  = -DPOSRES_B ; (Why ??)
>
>Did you read the paper I linked from the tutorial, which explains why this is 
>done for this very specific case?
>
>> ; Pull code
>> pull= yes
>> pull_ngroups= 2
>> pull_ncoords= 1
>> pull_group1_name= Chain_B
>> pull_group2_name= Chain_A
>> pull_coord1_type= umbrella  ; harmonic biasing force
>> pull_coord1_geometry= distance  ; simple distance increase
>> pull_coord1_groups  = 1 2
>> pull_coord1_dim = N N Y
>> pull_coord1_rate= 0.0
>> pull_coord1_k   = 1000  ; kJ mol^-1 nm^-2
>> pull_coord1_start   = yes   ; define initial COM distance > 0
>>
>>
>>
>> Conformations in Justin's tutorial are from steered MD. However, my 
>> conformations are not from SMD, and I have not done SMD on this system. So, 
>> how to define pull_group1 and pull_group2? And pull_coord1_geometry still 
>> set to "distance" ?
>
>The pull groups don't depend on where the configurations came from.  They 
>define 
>the reaction coordinate.  You can use whatever pull geometry makes sense; in 
>the 
>tutorial it is a simple linear reaction coordinate directly along the z-axis. 
>Other applications may require different definitions.
>
>> Also, need I fix any part of protein in umbrella sampling (with " -DPOSRES 
>> ") ? Why?
>
>Generally, no, but you haven't given any useful detail about what your 
>simulation system is.
>
>-Justin
>
>-- 
>==
>
>Justin A. Lemkul, Ph.D.
>Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
>Department of Pharmaceutical Sciences
>School of Pharmacy
>Health Sciences Facility II, Room 629
>University of Maryland, Baltimore
>20 Penn St.
>Baltimore, MD 21201
>
>jalem...@outerbanks.umaryland.edu | (410) 706-7441
>http://mackerell.umaryland.edu/~jalemkul
>
>==
>-- 
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[gmx-users] How to write pull code in umbrella sampling

[Qing Lv]

Dear Colleagues,


I am trying to do an umbrella sampling using a series of conformations 
extracted from several unbiased MD trajectories. But I am not sure about the 
pull code in .mdp file.
Below is the pull code from the tutorial of Dr. Justin Lemkul :
define  = -DPOSRES_B ; (Why ??)
; Pull code 
pull= yes   
pull_ngroups= 2
pull_ncoords= 1
pull_group1_name= Chain_B
pull_group2_name= Chain_A
pull_coord1_type= umbrella  ; harmonic biasing force
pull_coord1_geometry= distance  ; simple distance increase
pull_coord1_groups  = 1 2
pull_coord1_dim = N N Y
pull_coord1_rate= 0.0
pull_coord1_k   = 1000  ; kJ mol^-1 nm^-2
pull_coord1_start   = yes   ; define initial COM distance > 0



Conformations in Justin's tutorial are from steered MD. However, my 
conformations are not from SMD, and I have not done SMD on this system. So, how 
to define pull_group1 and pull_group2? And pull_coord1_geometry still set to 
"distance" ?
Also, need I fix any part of protein in umbrella sampling (with " -DPOSRES ") ? 
Why?
Any one can provide a template of pull code for such simulations?


Thanks a lot
Qing Lv


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[gmx-users] GMX 2016 compiling problem (libgromacs.so.2.1.0: undefined reference to `GOMP_parallel')

[Qing Lv]

Dear Colleagues,

I am now compiling GMX 2016.1 on CentOS 6, with devtoolset-3 and -4. When 
executing 'make' , I got such errors:

[ 98%] Building CXX object share/template/CMakeFiles/template.dir/template.cpp.o
Linking CXX executable ../../bin/template
../../lib/libgromacs.so.2.1.0: undefined reference to `GOMP_parallel'
collect2: error: ld returned 1 exit status
make[2]: *** [bin/template] Error 1
make[1]: *** [share/template/CMakeFiles/template.dir/all] Error 2
make: *** [all] Error 2

Any one can help? Thank you!
Qing
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[gmx-users] Problems of compiling GMX 2016.1 on CygWin

[Qing Lv]

Hi,


I am trying to compile GMX 2016.1 on CygWin, but failed.


   mkdir build
   cd build
   cmake .. -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs2016.1 
-DGMX_BUILD_OWN_FFTW=ON
   make
/tmp/cctDFyCD.s: Assembler messages:
/tmp/cctDFyCD.s:49: Error: invalid register for .seh_savexmm
Makefile:745: recipe for target 'n1fv_5.lo' failed
make[8]: *** [n1fv_5.lo] Error 1
Makefile:501: recipe for target 'all' failed
make[7]: *** [all] Error 2
Makefile:382: recipe for target 'all-recursive' failed
make[6]: *** [all-recursive] Error 1
Makefile:494: recipe for target 'all-recursive' failed
make[5]: *** [all-recursive] Error 1
Makefile:672: recipe for target 'all-recursive' failed
make[4]: *** [all-recursive] Error 1
Makefile:536: recipe for target 'all' failed
make[3]: *** [all] Error 2
src/contrib/fftw/CMakeFiles/fftwBuild.dir/build.make:110: recipe for target 
'src/contrib/fftw/fftwBuild-prefix/src/fftwBuild-stamp/fftwBuild-build' failed
make[2]: *** 
[src/contrib/fftw/fftwBuild-prefix/src/fftwBuild-stamp/fftwBuild-build] Error 2
CMakeFiles/Makefile2:1088: recipe for target 
'src/contrib/fftw/CMakeFiles/fftwBuild.dir/all' failed
make[1]: *** [src/contrib/fftw/CMakeFiles/fftwBuild.dir/all] Error 2
Makefile:147: recipe for target 'all' failed
make: *** [all] Error 2


I searched Google and the maillist but did not find the solutions. Anyone may 
help? (Actually I just compiled GMX 5.1.4 on CygWin on the same computer, and 
no errors occurred.)


Thanks,
Qing
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Re: [gmx-users] Errors in building GMX 5.1.x on Redhat 6.5 (a lot of "Undefined reference to ..")

[Qing Lv]

Dear Mark,


I built and ran it on the same machine.
The test conclusion of $builddir/bin/mdrun-test is:
[--] Global test environment tear-down
[==] 24 tests from 8 test cases ran. (5206 ms total)
[  PASSED  ] 24 tests.


I searched the complete test result of mdrun-rest (which is quite long), but 
did not find "SIMD" (or Simd, simd).
Thanks.


Qing


At 2017-02-03 21:12:15, "Mark Abraham" <mark.j.abra...@gmail.com> wrote:
>Hi,
>
>Surprising, but we don't test on (or officially support) Cygwin, so could
>happen. It would be most likely to happen if you built on a different
>machine than you were running on... Does $builddir/bin/mdrun-test pass?
>Does the terminal output mention SIMD?
>
>Mark
>
>On Fri, Feb 3, 2017 at 1:29 PM Qing Lv <lvqingjie...@163.com> wrote:
>
>> Mark,
>>
>>
>> The results are:
>> $ ./simd-test.exe
>> Segmentation fault (core dumped)
>>
>>
>> Thanks,
>> Qing
>>
>>
>> At 2017-02-03 19:46:35, "Mark Abraham" <mark.j.abra...@gmail.com> wrote:
>> >Hi,
>> >
>> >Unlikely, given that the other tests passed. But what is the output from
>> >running that manually, e.g. $builddir/bin/simd-test
>> >
>> >Mark
>> >
>> >On Fri, Feb 3, 2017 at 6:52 AM Qing Lv <lvqingjie...@163.com> wrote:
>> >
>> >> Thank you, Mark. I am now trying to install devtoolset-2.
>> >>
>> >>
>> >> Regarding Cygwin version, I must clarify that, although the compilation
>> is
>> >> successful, I got an error message when performing "make check":
>> >> 95% tests passed, 1 tests failed out of 20
>> >> The following tests FAILED:
>> >> 12 - SimdUnitTests (SEGFAULT)
>> >> Will it be a serious problem?
>> >> Thanks.
>> >>
>> >>
>> >> Qing
>> >>
>> >>
>> >> At 2017-02-03 13:08:50, "Mark Abraham" <mark.j.abra...@gmail.com>
>> wrote:
>> >> >Hi,
>> >> >
>> >> >These are linking errors that look like they are from not linking the
>> >> >appropriate version of the C++ standard library. I highly recommend
>> >> leaving
>> >> >the system libraries alone on redhat systems, and instead compiling
>> with
>> >> >the devtoolset packages.
>> >> >
>> >> >Thanks for the Cygwin report. People often report problems that look
>> like
>> >> >they come from broken systems, and we rarely hear of a resolution.
>> >> >
>> >> >Mark
>> >> >
>> >> >On Fri, 3 Feb 2017 05:55 Qing Lv <lvqingjie...@163.com> wrote:
>> >> >
>> >> >> Hi Colleagues,
>> >> >>
>> >> >>
>> >> >> I am trying to build GMX 5.1.x (tried 5.1.4, 5.1.1, & 5.1) on a
>> Redhat
>> >> 6.5
>> >> >> server; I have updated GCC compiler and all dependent libraries
>> (tried
>> >> GCC
>> >> >> 4.9.4 and GCC 6.3.0). (The built-in compiler of Redhat 6.5 is GCC
>> 4.4.7,
>> >> >> which is too old.)
>> >> >> I used the commmand
>> >> >> export CC=gcc
>> >> >> export CXX=gcc
>> >> >> cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
>> >> >> # No errors reported till now
>> >> >> make
>> >> >> When 100% completed, I got a lot of error messages like
>> >> >> ../../lib/libgromacs.so.1.0.0: Undefined reference to
>> >> >> ‘std::runtime_error::what() const’
>> >> >> ../../lib/libgromacs.so.1.0.0: Undefined reference to 
>> >> >> ../../lib/libgromacs.so.1.0.0: Undefined reference to 
>> >> >> And the error messages finished with
>> >> >> collect2: Error: ld returns 1
>> >> >> make[2]: *** [bin/template] Error 1
>> >> >> make[1]: *** [share/template/CMakeFiles/template.dir/all] Error 2
>> >> >> make: *** [all] Error 2
>> >> >>
>> >> >>
>> >> >> Any friends can help? Thanks
>> >> >> BTW, I have just successfully compiled GMX 5.1.4 on Cygwin.
>> >> >>
>> >> >>
>> >> >> Qing
>> >> >> --
>> >> >> Gromacs Users mailing list
>> >> >

Re: [gmx-users] Errors in building GMX 5.1.x on Redhat 6.5 (a lot of "Undefined reference to ..")

[Qing Lv]

Mark,


The results are:
$ ./simd-test.exe
Segmentation fault (core dumped)


Thanks,
Qing


At 2017-02-03 19:46:35, "Mark Abraham" <mark.j.abra...@gmail.com> wrote:
>Hi,
>
>Unlikely, given that the other tests passed. But what is the output from
>running that manually, e.g. $builddir/bin/simd-test
>
>Mark
>
>On Fri, Feb 3, 2017 at 6:52 AM Qing Lv <lvqingjie...@163.com> wrote:
>
>> Thank you, Mark. I am now trying to install devtoolset-2.
>>
>>
>> Regarding Cygwin version, I must clarify that, although the compilation is
>> successful, I got an error message when performing "make check":
>> 95% tests passed, 1 tests failed out of 20
>> The following tests FAILED:
>> 12 - SimdUnitTests (SEGFAULT)
>> Will it be a serious problem?
>> Thanks.
>>
>>
>> Qing
>>
>>
>> At 2017-02-03 13:08:50, "Mark Abraham" <mark.j.abra...@gmail.com> wrote:
>> >Hi,
>> >
>> >These are linking errors that look like they are from not linking the
>> >appropriate version of the C++ standard library. I highly recommend
>> leaving
>> >the system libraries alone on redhat systems, and instead compiling with
>> >the devtoolset packages.
>> >
>> >Thanks for the Cygwin report. People often report problems that look like
>> >they come from broken systems, and we rarely hear of a resolution.
>> >
>> >Mark
>> >
>> >On Fri, 3 Feb 2017 05:55 Qing Lv <lvqingjie...@163.com> wrote:
>> >
>> >> Hi Colleagues,
>> >>
>> >>
>> >> I am trying to build GMX 5.1.x (tried 5.1.4, 5.1.1, & 5.1) on a Redhat
>> 6.5
>> >> server; I have updated GCC compiler and all dependent libraries (tried
>> GCC
>> >> 4.9.4 and GCC 6.3.0). (The built-in compiler of Redhat 6.5 is GCC 4.4.7,
>> >> which is too old.)
>> >> I used the commmand
>> >> export CC=gcc
>> >> export CXX=gcc
>> >> cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
>> >> # No errors reported till now
>> >> make
>> >> When 100% completed, I got a lot of error messages like
>> >> ../../lib/libgromacs.so.1.0.0: Undefined reference to
>> >> ‘std::runtime_error::what() const’
>> >> ../../lib/libgromacs.so.1.0.0: Undefined reference to 
>> >> ../../lib/libgromacs.so.1.0.0: Undefined reference to 
>> >> And the error messages finished with
>> >> collect2: Error: ld returns 1
>> >> make[2]: *** [bin/template] Error 1
>> >> make[1]: *** [share/template/CMakeFiles/template.dir/all] Error 2
>> >> make: *** [all] Error 2
>> >>
>> >>
>> >> Any friends can help? Thanks
>> >> BTW, I have just successfully compiled GMX 5.1.4 on Cygwin.
>> >>
>> >>
>> >> Qing
>> >> --
>> >> 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
>> >
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>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
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>> send a mail to gmx-users-requ...@gromacs.org.
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Re: [gmx-users] Errors in building GMX 5.1.x on Redhat 6.5 (a lot of "Undefined reference to ..")

[Qing Lv]

Thank you, Mark. I am now trying to install devtoolset-2.


Regarding Cygwin version, I must clarify that, although the compilation is 
successful, I got an error message when performing "make check":
95% tests passed, 1 tests failed out of 20
The following tests FAILED:
12 - SimdUnitTests (SEGFAULT)
Will it be a serious problem?
Thanks.


Qing


At 2017-02-03 13:08:50, "Mark Abraham" <mark.j.abra...@gmail.com> wrote:
>Hi,
>
>These are linking errors that look like they are from not linking the
>appropriate version of the C++ standard library. I highly recommend leaving
>the system libraries alone on redhat systems, and instead compiling with
>the devtoolset packages.
>
>Thanks for the Cygwin report. People often report problems that look like
>they come from broken systems, and we rarely hear of a resolution.
>
>Mark
>
>On Fri, 3 Feb 2017 05:55 Qing Lv <lvqingjie...@163.com> wrote:
>
>> Hi Colleagues,
>>
>>
>> I am trying to build GMX 5.1.x (tried 5.1.4, 5.1.1, & 5.1) on a Redhat 6.5
>> server; I have updated GCC compiler and all dependent libraries (tried GCC
>> 4.9.4 and GCC 6.3.0). (The built-in compiler of Redhat 6.5 is GCC 4.4.7,
>> which is too old.)
>> I used the commmand
>> export CC=gcc
>> export CXX=gcc
>> cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
>> # No errors reported till now
>> make
>> When 100% completed, I got a lot of error messages like
>> ../../lib/libgromacs.so.1.0.0: Undefined reference to
>> ‘std::runtime_error::what() const’
>> ../../lib/libgromacs.so.1.0.0: Undefined reference to 
>> ../../lib/libgromacs.so.1.0.0: Undefined reference to 
>> And the error messages finished with
>> collect2: Error: ld returns 1
>> make[2]: *** [bin/template] Error 1
>> make[1]: *** [share/template/CMakeFiles/template.dir/all] Error 2
>> make: *** [all] Error 2
>>
>>
>> Any friends can help? Thanks
>> BTW, I have just successfully compiled GMX 5.1.4 on Cygwin.
>>
>>
>> Qing
>> --
>> 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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[gmx-users] Errors in building GMX 5.1.x on Redhat 6.5 (a lot of "Undefined reference to ..")

[Qing Lv]

Hi Colleagues,


I am trying to build GMX 5.1.x (tried 5.1.4, 5.1.1, & 5.1) on a Redhat 6.5 
server; I have updated GCC compiler and all dependent libraries (tried GCC 
4.9.4 and GCC 6.3.0). (The built-in compiler of Redhat 6.5 is GCC 4.4.7, which 
is too old.)
I used the commmand
export CC=gcc
export CXX=gcc
cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON   
   # No errors reported till now
make
When 100% completed, I got a lot of error messages like
../../lib/libgromacs.so.1.0.0: Undefined reference to 
‘std::runtime_error::what() const’
../../lib/libgromacs.so.1.0.0: Undefined reference to 
../../lib/libgromacs.so.1.0.0: Undefined reference to 
And the error messages finished with
collect2: Error: ld returns 1
make[2]: *** [bin/template] Error 1
make[1]: *** [share/template/CMakeFiles/template.dir/all] Error 2
make: *** [all] Error 2


Any friends can help? Thanks
BTW, I have just successfully compiled GMX 5.1.4 on Cygwin.


Qing
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Re: [gmx-users] reproducibility of trajectory

[Qing Lv]

Thank you, Mark. Got it.

Qing


At 2015-08-19 17:32:22, Mark Abraham mark.j.abra...@gmail.com wrote:
Hi,

You've observed a single event. By itself that doesn't mean much of
anything. If you were in a car crash today, that doesn't mean you will be
in one every time you go on the road. But if you observe yourself in a car
crash every day, now you have evidence that you need driving lessons... If
you had a car crash once every hundred days, and reported only that single
day as evidence you need lessons... that'd be wrong on many levels.

Mark

On Wed, Aug 19, 2015 at 10:31 AM Qing Lv lvqingjie...@163.com wrote:

 Hi,

 I did a 200-ns MD for a protein and found an interesting conformation
 transition, and according to NMR study in literature, it is believed that
 10 us ~ ms scale simulations are needed to get this conformation transition.
 However, when I tried to reproduce this conformation transition, I was not
 so lucky any more... I repeated 6 x 200ns trajectories but failed to
 reproduce, even I used the same seed number.
 Do you have any ideas on this? Is it sufficient to present this result in
 papers, since I just got 1 trajectory?

 Thanks,
 Qing



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[gmx-users] reproducibility of trajectory

[Qing Lv]

Hi,

I did a 200-ns MD for a protein and found an interesting conformation 
transition, and according to NMR study in literature, it is believed that 10 us 
~ ms scale simulations are needed to get this conformation transition.
However, when I tried to reproduce this conformation transition, I was not so 
lucky any more... I repeated 6 x 200ns trajectories but failed to reproduce, 
even I used the same seed number.
Do you have any ideas on this? Is it sufficient to present this result in 
papers, since I just got 1 trajectory?

Thanks,
Qing



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[gmx-users] reproducibility of trajectory

[Qing Lv]

Hi,

I did a 200-ns MD for a protein and found an interesting conformation 
transition, and according to NMR study in literature, it is believed that 10 us 
~ ms scale simulations are needed to get this conformation transition.
However, when I tried to reproduce this conformation transition, I was not so 
lucky any more... I repeated 6 x 200ns trajectories but failed to reproduce, 
even I used the same seed number.
Do you have any ideas on this? Is it sufficient to present this result in 
papers, since I just got 1 trajectory?

Thanks,
Qing
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Re: [gmx-users] How to justify when the trajectory reached equilibrium

[Qing Lv]

I see. Thanks.

Qing



At 2015-07-11 05:07:27, Justin Lemkul jalem...@vt.edu wrote:


On 7/9/15 11:00 PM, Qing Lv wrote:
 It means to evaluate quantities over successive blocks of time (e.g. using 
 -b and -e that all GROMACS analysis tools support) and check to see whether 
 or not the quantities of interest are varying over time or if they are 
 stable, i.e. converged.


 Thank you, Justin.
 What size of blocks I need to divide in such an analysis? e.g., for a 100-ns 
 trajectory, is it appropriate to divide it into 5-ns or 10-ns blocks to see 
 if it has converged?


There are no hard and fast rules here.  It all depends on the frequency of 
your 
sampling and the time scale of the behavior(s) of interest.  Only you can 
figure 
those things out based on the goals of your work and your protocols for 
collecting data.

-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
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Re: [gmx-users] How to justify when the trajectory reached equilibrium

[Qing Lv]

Thank you, Justin.
I am trying to simulate a protein-ligand complex to see the conformation 
transition during the simulation... We propose that the receptor pocket may be 
subject to a conformational change upon ligand-binding, so I want to verify it 
by MD...
I am really a newbie in molecular simulation and all I did to analysis were 
time evolution of RMSD, interaction energy, and visualization. I try to do some 
principal component analysis, but literature said that PCA must be performed 
after equilibrium...

Could you give me more info on block-averaging, or any other advice that will 
help?

Best,
Qing


At 2015-07-09 19:41:09, Justin Lemkul jalem...@vt.edu wrote:


On 7/8/15 9:48 PM, Qing Lv wrote:
 Hi,

 I did a 70-ns MD simulation. I wonder how to justify when the trajectory 
 reached equilibrium...
 Seen from RMSD-time curve of C-alpha, the curve reached about 1 nm at 12 ns 
 and kept stable after that. Could I justify that the system reached 
 equilibrium at 12 ns? Are there any methods/criteria to justify the 
 equilibrium other than RMSD evolution?


RMSD is pretty useless in telling you anything about convergence.  Great, your 
structure probably isn't changing a whole lot (but RMSD can also hide 
interesting things).  Assess convergence based on the quantities of interest - 
why did you do the simulation?  What behavior are you trying to observe, and 
what measurables do you use to assess it?  If those metrics are invariant with 
time (e.g. via block-averaging or something) then your simulation is likely 
converged.

-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] on trjconv command

[Qing Lv]

Hi Brett,

I think the following command will work:
trjconv -f source.xtc -skip 5 -o target.xtc

Qing



At 2015-07-10 10:10:39, Brett brettliu...@163.com wrote:
Dear All,


Will you please show me the command based on the following cited content from 
the website on how to convert a xtc file with 1 frame per 2 ps to a xtc file 
with 1 frame per 10 ps? I hope the command contains “-dt” and “-timestep”， and 
what the values should be for  “-dt” and “-timestep”.


Best regards


Brett


With -dt it is possible to reduce the number of frames in the output. This 
option relies on the accuracy of the times in your input trajectory, so if 
these are inaccurate use the -timestep option to modify the time (this can be 
done simultaneously).
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Re: [gmx-users] How to justify when the trajectory reached equilibrium

[Qing Lv]

 It means to evaluate quantities over successive blocks of time (e.g. using -b 
 and -e that all GROMACS analysis tools support) and check to see whether or 
 not the quantities of interest are varying over time or if they are stable, 
 i.e. converged.


Thank you, Justin.
What size of blocks I need to divide in such an analysis? e.g., for a 100-ns 
trajectory, is it appropriate to divide it into 5-ns or 10-ns blocks to see if 
it has converged?

Qing




At 2015-07-10 01:39:42, Justin Lemkul jalem...@vt.edu wrote:


On 7/9/15 10:11 AM, Qing Lv wrote:
 Thank you, Justin.
 I am trying to simulate a protein-ligand complex to see the conformation 
 transition during the simulation... We propose that the receptor pocket may 
 be subject to a conformational change upon ligand-binding, so I want to 
 verify it by MD...
 I am really a newbie in molecular simulation and all I did to analysis were 
 time evolution of RMSD, interaction energy, and visualization. I try to do 
 some principal component analysis, but literature said that PCA must be 
 performed after equilibrium...


If you are hypothesizing a conformational change, then you need a way to 
quantify that change - distances, angles, etc.

 Could you give me more info on block-averaging, or any other advice that 
 will help?


It means to evaluate quantities over successive blocks of time (e.g. using -b 
and -e that all GROMACS analysis tools support) and check to see whether or 
not 
the quantities of interest are varying over time or if they are stable, i.e. 
converged.

-Justin

-- 
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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

==
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[gmx-users] How to justify when the trajectory reached equilibrium

[Qing Lv]

Hi,

I did a 70-ns MD simulation. I wonder how to justify when the trajectory 
reached equilibrium...
Seen from RMSD-time curve of C-alpha, the curve reached about 1 nm at 12 ns and 
kept stable after that. Could I justify that the system reached equilibrium at 
12 ns? Are there any methods/criteria to justify the equilibrium other than 
RMSD evolution?

Thanks a lot,
Qing

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[gmx-users] How to justify when the trajectory reached equilibrium

[Qing Lv]

Hi,

I did a 70-ns MD simulation. I wonder how to justify when the trajectory 
reached equilibrium...
Seen from RMSD-time curve of C-alpha, the curve reached about 1 nm at 12 ns and 
kept stable after that. Could I justify that the system reached equilibrium at 
12 ns? Are there any methods/criteria to justify the equilibrium other than 
RMSD evolution?

Thanks a lot,
Qing
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