[gmx-users] Why are the bond and angle energy at the first step of energy minimization not equal 0?
Hi Gromacs user, I am following a Gromacs tutorial on the website of Dr. Justin: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/05_EM.html After performing energy minimization, I open the log file and see that at time step = 0 (time = 0.000), bond energy and angle energy are not equal 0. Given that: E_bond = 0.5*k*(r-r0)^2 At t = 0: r = r0, therefore E_bond should be approximate 0. Please correct me. Thank you. Best regards, *Lan Hoa* -- 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] Why are the bond and angle energy at the first step of energy minimization not equal 0?
Great explanation! Thank you very much. *Lan Hoa* 2018-03-17 13:02 GMT-05:00 Justin Lemkul : > > > On 3/17/18 1:56 PM, Hoa Trinh wrote: > >> Hi Gromacs user, >> I am following a Gromacs tutorial on the website of Dr. Justin: >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx >> -tutorials/lysozyme/05_EM.html >> >> After performing energy minimization, I open the log file and see that at >> time step = 0 (time = 0.000), bond energy and angle energy are not equal >> 0. >> Given that: E_bond = 0.5*k*(r-r0)^2 >> At t = 0: r = r0, therefore E_bond should be approximate 0. >> Please correct me. >> > > Simply, r =/= r0 at t = 0 (and in energy minimization it's not time, it's > step number). > > Unless a structure was built *exactly* according to the force field > parameters in terms of equilibrium bond lengths and valence angles, you > will never have a zero value for these terms. Experimental structures > certainly never conform exactly to these parameters, nor will they > throughout the simulation. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.biochem.vt.edu/people/faculty/JustinLemkul.html > > == > > -- > 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] Listed nonbonded interaction between particles beyond the table limit.
Dear Gromacs experts, I do aware that this question has been repeated many times in the mailing list and I do go through all of answers. However, I still cannot find the answer for my problem. When I run on single node on my laptop, the simulation goes well and the warning does not appear. When I run on single node on a cluster, the warning appears but the simulation keep running. When I run on many nodes, the warning appears and the simulation stops. If my initial system is unstable, the simulation should blow up and the warning should appear when I run on my laptop. So what is the reason? I am looking forward to hearing from you. Thank you very much in advance. Best regards, *Lan Hoa* -- 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] Improper dihedral angle: -30 degree or (360-30) degree
Dear Gromacs community, I'd like to know what is the range of improper dihedral angle, [0,pi] , [0,2pi] or [-pi, pi] ? For example, if I have an angle belonging to quadrant IV, should the angle be -30 or (360-30) or (180-30) degree? I appreciate your help. Best regards, *Lan Hoa* -- 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] Improper dihedral angle: -30 degree or (360-30) degree
Dear Mark, I read the chapter more than 3 times already, what I found is just "Note that in the input in topology files, angles are given in degrees and force constants in kJ/mol/rad 2 ." *Lan Hoa* 2017-09-10 7:19 GMT-05:00 Mark Abraham : > Hi, > > Check out the sections in chapter four of the reference manual. > > Mark > > On Sun, 10 Sep 2017 13:36 Hoa Trinh wrote: > > > Dear Gromacs community, > > I'd like to know what is the range of improper dihedral angle, [0,pi] , > > [0,2pi] or [-pi, pi] ? For example, if I have an angle belonging to > > quadrant > > IV, should the angle be -30 or (360-30) or (180-30) degree? > > I appreciate your help. > > Best regards, > > *Lan Hoa* > > -- > > 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] Equilibration at each temperature in simmulated annealing
Hi all, I would like to cool my system from 200K to 100K via multiple intermediate temperatures and at each temperature, the system is equilibrated for a while before decreasing temperature. I am thinking of doing something like this: annealing_temp = 200 150 150 100 100 But I am afraid this is not going to equilibrate my system at 150K since I only have one value of t_couple in mdp file. That means I can only choose to equilibrate my system at either 150K or 100K. So how can I equilibrate my system at each temperature in simulated annealing? I am looking forward to hearing from you. Thanks in advance! Best regards, *Lan Hoa* -- 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 angle. Select many groups at one time.
Dear Gromacs community, I'd like to use gmx angle tool of Gromacs. How can I select many groups at one time so that I will have the angle distribution for all groups? Thanks in advance. Best regards, *Lan Hoa* -- 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] How to turn of setting of OpenMP threads in Gromacs 5.0.7
Hi, I'd like to turn off the setting of OpenMP threads in Gromacs 5.0.7. When I run cmake, I already disable GMX_OPENMP. After that I checked "CMakeCache.txt" file and see that: //Enable OpenMP-based multithreading GMX_OPENMP:BOOL=OFF However, when I use the command gmx mdrun -v -deffnm I still see Gromacs notify that: Using 4 OpenMP threads I just don't want to use multiple threads. Thank you very much in advance. Best regards, *Lan Hoa* -- 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] How to turn of setting of OpenMP threads in Gromacs 5.0.7
Thanks, Quyen. After using "ntom " option, I can set the number of OpenMP threads. Best, *Lan Hoa* 2017-10-14 10:25 GMT-05:00 Quyen V. Vu : > Hi Hoa, > have you try: -ntomp with mdrun? > Best, > Quyen > -- > 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] A debugger to detect the reason of segmentation fault of Gromacs
Hi, Can anyone please recommend debuggers to detect the reason of segmentation fault of Gromacs? Thank you very much in advance. Best, *Lan Hoa* -- 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] A debugger to detect the reason of segmentation fault of Gromacs
Dear Mark, I am working on a project which requires me to modify the source code of Gromacs to include a potential energy which Gromacs doesn't have. The segmentation fault happens immediately at the first step of minimization with Gromacs 5.0.7 and the force was reported to be 0. My system is just a coarse-grained of protein which contains ~ 100 beads in the vacuum, I already tested it with the modifed source code of Gromacs version 4 and it works just fine. As a novice, I might have done something wrong with the source code. As you said, gdb is not much of help but I think it worths a try. Thank you. *Lan Hoa* 2017-10-14 13:16 GMT-05:00 Mark Abraham : > Hi, > > Anything is fine, e.g. gdb is widely available. But you are unlikely to > learn anything actionable. Most people's segfaults are because of one of > the cases of http://www.gromacs.org/Documentation/Terminology/Blowing_Up > because > their model and/or their starting configuration are somehow not > appropriate. Why do you think your case might be different? > > Mark > > On Sat, Oct 14, 2017 at 7:16 PM Hoa Trinh wrote: > > > Hi, > > Can anyone please recommend debuggers to detect the reason of > segmentation > > fault of Gromacs? > > Thank you very much in advance. > > Best, > > *Lan Hoa* > > -- > > 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] Meaning of GMX?
Dear GMX users, Why does Gromacs have many gmx functions: gmx grompp gmx mdrun ... What is the meaning of GMX? Best, *Lan Hoa* -- 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] Calculated bonded interactions - number of bonds- bondfree.c
Hi all,
I am trying to look into the source code of Gromacs 5.0.7 to see how
Gromacs calculate bonded interactions. For example, to calculate bond
interaction between 2 atoms, there is the function (gmxlib/bondfree.c):
real bonds(int nbonds, ...)
{
for (i = 0; (i < nbonds); )
{
type = forceatoms[i++];
ai = forceatoms[i++];
aj = forceatoms[i++];
}
Is "nbonds" the total number of bond interactions? In my topology file, I
have 126 pairs in the [ bonds ] section. However, when I printf the
variable nbonds, it appears to be 378. I have no idea why. Can anyone
please help me to explain what is nbonds?
Thank you very much in advance.
Best regards,
*Lan Hoa*
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Re: [gmx-users] Calculated bonded interactions - number of bonds- bondfree.c
Dear Mark & Justin,
Thank you very much. Hum, the name of variable nbonds is a bit misleading.
*Lan Hoa*
2017-10-26 6:10 GMT-05:00 Justin Lemkul :
>
>
> On 10/26/17 1:56 AM, Hoa Trinh wrote:
>
>> Hi all,
>> I am trying to look into the source code of Gromacs 5.0.7 to see how
>> Gromacs calculate bonded interactions. For example, to calculate bond
>> interaction between 2 atoms, there is the function (gmxlib/bondfree.c):
>> real bonds(int nbonds, ...)
>> {
>>
>>for (i = 0; (i < nbonds); )
>> {
>> type = forceatoms[i++];
>> ai = forceatoms[i++];
>> aj = forceatoms[i++];
>>
>> }
>> Is "nbonds" the total number of bond interactions? In my topology file, I
>> have 126 pairs in the [ bonds ] section. However, when I printf the
>> variable nbonds, it appears to be 378. I have no idea why. Can anyone
>> please help me to explain what is nbonds?
>>
>
> 378 = 126 * 3
>
> nbonds here indicates the size of the array, which holds (type, ai, aj)
> for each bond in the system.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
>
> --
> 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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> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
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[gmx-users] Compilation error - Gromacs 2016.4
Dear GMX users, I encountered the following error when compiling Gromacs 2016.4: error: expected primary-expression before ‘>’ token k_S = load(coeff); Does anyone face the same situation? What is the solution? Thanks in advance. Best regards, *Lan Hoa* -- 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] Compilation error - Gromacs 2016.4
Dear Mark, Your guess is great :) Thanks for advising me to use version control. Best regards, *Lan Hoa* 2017-11-13 18:18 GMT-06:00 Mark Abraham : > Hi, > > That should never happen - which compiler was it? and are you sure this is > unmodified 2016.4? > > Mark > > On Mon, Nov 13, 2017 at 3:17 PM Hoa Trinh wrote: > > > Dear GMX users, > > I encountered the following error when compiling Gromacs 2016.4: > > > > error: expected primary-expression before ‘>’ token > > k_S = load(coeff); > > > > > > Does anyone face the same situation? What is the solution? > > Thanks in advance. > > Best regards, > > > > *Lan Hoa* > > -- > > 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] Generate non-bonded combinations
Dear Gromacs community, I am using Gromacs to simulate a C-alpha structure and have the following topology file (created by http://smog-server.org/). [ defaults ] ;nbfunc comb-rule gen-pairs 1 1 no [ atomtypes ] ;name mass charge ptype c10 c12 CA 1.0000.000 A0.000 0.167772160E-04 [ moleculetype ] ;name nrexcl Macromolecule 3 [ atoms ] ;nr type resnr residue atom cgnr charge mass 1 CA 1 ASN CA 1 0.000 1.000 2 CA 2 LEU CA 2 0.000 1.000 3 CA 3 LYS CA 3 0.000 1.000 4 CA 4 THR CA 4 0.000 1.000 [ pairs ] ; i j type and weights 2 25 1 0.198921701E+01 0.132925132E+01 2 27 1 0.582768432E+02 0.765215442E+02 2 45 1 0.865830453E+01 0.776440056E+01 3 7 1 0.143745898E+02 0.142660275E+02 3 8 1 0.458838723E+02 0.574355228E+02 ... As I understand, VDW parameter will only be generated by grompp for pairs of atoms which are defined in the directive [pairs]. When I use grompp, the notification is: Generated 1 of the 1 non-bonded parameter combinations. Based on the above topology ([pairs]) i expected there are more non-bonded combination generated. Can anyone help me to explain this? Also: [ atomtypes ] ;name mass charge ptype c10 c12 CA 1.0000.000 A0.000 0.167772160E-04 At first, I thought it meant that the pairs which were not defined in the directive [pairs] will be repulsive only, but they choose genpairs=no, so it looks like there is nothing to do with the lines?? Please help me! Thanks in advance. Best regards, *Lan Hoa * -- 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] Topology file and itp file
Dear All, I am modelling a system of spherical beads (which I named as Fi) which only repulsive each other. I would highly appreciate if some one can have a look at the following topology which I created: (ficoll1.top) [ defaults ] ;nbfunc comb-rule gen-pairs 1 1 no [ atomtypes ] ;name mass charge ptype c10 c12 Fi 6.0000.000 A0.000 14000 [ moleculetype ] ;name nrexcl Ficoll 0 [atoms] ;nr type resnr residue atom cgnr charge mass 1 Fi 1 Fi Fi 1 0.000 6.000 [ system ] ; name Ficoll [molecules] ; namenumber Ficoll 64 I also created another topology: (ficoll2.top) [ defaults ] ;nbfunc comb-rule gen-pairs 1 1 no #include "fi.itp" [ system ] ; name Ficoll [molecules] ; namenumber Ficoll 64 where fi.itp is the following: [ atomtypes ] ;name mass charge ptype c10 c12 Fi 6.0000.000 A0.000 14000 [ moleculetype ] ;name nrexcl Ficoll 0 [atoms] ;nr type resnr residue atom cgnr charge mass 1 Fi 1 Fi Fi 1 0.000 6.000 I expected that the simulation with the 2 topology files should gave the same results but they gave the different results, I don't understand what is wrong here. Thank you very much in advance. Best regards, *Lan Hoa* -- 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] Topology file and itp file
Dear Mark, I equilibrated my system in NVT, and then plot the potential energy. However the potential energy created with the two topology is not match. Thanks in advance, Best regards, *Lan Hoa* 2017-04-20 14:25 GMT-05:00 Mark Abraham : > Hi, > > How are you assessing "different?" > > Mark > > On Thu, 20 Apr 2017 21:13 lan hoa Trinh wrote: > > > Dear All, > > I am modelling a system of spherical beads (which I named as Fi) which > only > > repulsive each other. I would highly appreciate if some one can have a > look > > at the following topology which I created: > > (ficoll1.top) > > [ defaults ] > > ;nbfunc comb-rule gen-pairs > >1 1 no > > > > > > [ atomtypes ] > > ;name mass charge ptype c10 c12 > > Fi 6.0000.000 A0.000 14000 > > > > [ moleculetype ] > > ;name nrexcl > > Ficoll 0 > > > > [atoms] > > ;nr type resnr residue atom cgnr charge mass > > 1 Fi 1 Fi Fi 1 0.000 6.000 > > > > > > [ system ] > > ; name > > Ficoll > > > > [molecules] > > ; namenumber > > Ficoll 64 > > > > I also created another topology: > > (ficoll2.top) > > > > [ defaults ] > > ;nbfunc comb-rule gen-pairs > >1 1 no > > > > #include "fi.itp" > > > > [ system ] > > ; name > > Ficoll > > > > [molecules] > > ; namenumber > > Ficoll 64 > > > > where fi.itp is the following: > > [ atomtypes ] > > ;name mass charge ptype c10 c12 > > Fi 6.0000.000 A0.000 14000 > > > > [ moleculetype ] > > ;name nrexcl > > Ficoll 0 > > > > [atoms] > > ;nr type resnr residue atom cgnr charge mass > > 1 Fi 1 Fi Fi 1 0.000 6.000 > > > > I expected that the simulation with the 2 topology files should gave the > > same results but they gave the different results, > > > > I don't understand what is wrong here. > > Thank you very much in advance. > > Best regards, > > *Lan Hoa* > > -- > > 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] Topology file and itp file
Dear Justin, I don't understand what you meant by saying MD is chaotic. You mean about velocity? I know that when we generate velocity based on Boltzmann distribution, we have to generate random number. However, what we call random numbers is not actually "random" because they are obeying algorithm. I don't know if I understand correctly but if we start from an initial value, we generate a "seed", and then we have a "random" series of number. However next time, when we rerun the simulation, the same series will be created. *Lan Hoa* 2017-04-21 7:21 GMT-05:00 Justin Lemkul : > > > On 4/20/17 4:37 PM, lan hoa Trinh wrote: > >> Dear Mark, >> I equilibrated my system in NVT, and then plot the potential energy. >> However the potential energy created with the two topology is not match. >> Thanks in advance, >> > > MD is chaotic, and even identical topologies will yield different > results. If you want to test the equivalence of a topology, you should > evaluate a single-point energy of an identical configuration of atoms with > the two topologies. That's the only meaningful test. > > http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > == > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/Support > /Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Topology file and itp file
Dear Justin, I am assessing based on a time series. You are right :), even I used the same topology file, the change over time of the potential energy is still different. It is good to know ^&^ . All the information you provided are very helpful. Ok, let me try to express what I 've understood so far: When we assess a single point energy, if the two topology are the same, we will get the same value of energy at a single point (which could be the starting point or an arbitrary point of the trajectory). However, due to the non-producibility, even we get the same value of energy at each single point, it is not true when we try to simulate over a period of time and what we can trust is the the average value. Hum, do I understand wrongly again, hixx. Best regards, *Lan Hoa* 2017-04-22 20:41 GMT-05:00 Justin Lemkul : > > > On 4/22/17 9:06 PM, lan hoa Trinh wrote: > >> Dear Justin, >> I don't understand what you meant by saying MD is chaotic. You mean about >> velocity? I know that when we generate velocity based on Boltzmann >> distribution, we have to generate random number. However, what we call >> random numbers is not actually "random" because they are obeying >> algorithm. >> I don't know if I understand correctly but if we start from an initial >> value, we generate a "seed", and then we have a "random" series of number. >> However next time, when we rerun the simulation, the same series will be >> created. >> >> > This is not really what I was referring to at all. > > http://www.gromacs.org/Documentation/Terminology/Reproducibility > > What is not clear from your posts is really how you're assessing "same" > vs. "different" - you mention potential energy but you do not say what you > did. A time series? A single point energy? An average of some sort? If > your two simulations are too short to be considered converged, you will > probably get a different value. Whether that value means anything is an > open question. In the limit of ergodicity, a simple system like yours > should easily produce the same ensemble-average properties. But if you're > just testing whether or not your two topologies are the same, the only test > you need to do is what I suggested, a single-point energy. Compare apples > to apples. Or atoms to atoms, as it were :) > > -Justin > > *Lan Hoa* >> >> >> 2017-04-21 7:21 GMT-05:00 Justin Lemkul : >> >> >>> >>> On 4/20/17 4:37 PM, lan hoa Trinh wrote: >>> >>> Dear Mark, >>>> I equilibrated my system in NVT, and then plot the potential energy. >>>> However the potential energy created with the two topology is not match. >>>> Thanks in advance, >>>> >>>> >>> MD is chaotic, and even identical topologies will yield different >>> results. If you want to test the equivalence of a topology, you should >>> evaluate a single-point energy of an identical configuration of atoms >>> with >>> the two topologies. That's the only meaningful test. >>> >>> http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy >>> >>> -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. >>> >>> > -- > == > > 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...
Re: [gmx-users] Topology file and itp file
awesome :) Thank you! *Lan Hoa* 2017-04-23 20:15 GMT-05:00 Justin Lemkul : > > > On 4/22/17 10:39 PM, lan hoa Trinh wrote: > >> Dear Justin, >> I am assessing based on a time series. You are right :), even I used the >> same topology file, the change over time of the potential energy is still >> different. It is good to know ^&^ . All the information you provided are >> very helpful. Ok, let me try to express what I 've understood so far: >> When we assess a single point energy, if the two topology are the same, we >> will get the same value of energy at a single point (which could be the >> starting point or an arbitrary point of the trajectory). However, due to >> > > Correct. > > the non-producibility, even we get the same value of energy at each single >> point, it is not true when we try to simulate over a period of time and >> what we can trust is the the average value. >> > > Correct. > > -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] Space between the columns in the topology file of Gromacs
Dear Gromacs society, I wonder if there is the default for the space between the columns in the topology file, for example: [ bonds ] ;ai aj funcr0(nm) Kb 12 1 3.805916447e-01 2.0e+04 23 1 3.788218579e-01 2.0e+04 34 1 3.790369375e-01 2.0e+04 Should it be fixed that ai, aj at the fix positions, i.e. 8 spaces of tab size for example? I am looking forward to hearing from you. Best regards, *Lan Hoa* -- 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] Space between the columns in the topology file of Gromacs
Thank you, Best, *Lan Hoa* 2017-06-15 17:02 GMT-05:00 Mark Abraham : > Hi, > > Those are simply fields separated by whitespace. Columns not relevant. > > Mark > > On Thu, 15 Jun 2017 22:10 lan hoa Trinh wrote: > > > Dear Gromacs society, > > I wonder if there is the default for the space between the columns in the > > topology file, for example: > > [ bonds ] > > ;ai aj funcr0(nm) Kb > > 12 1 3.805916447e-01 2.0e+04 > > 23 1 3.788218579e-01 2.0e+04 > > 34 1 3.790369375e-01 2.0e+04 > > > > Should it be fixed that ai, aj at the fix positions, i.e. 8 spaces of > tab > > size for example? > > I am looking forward to hearing from you. > > Best regards, > > *Lan Hoa* > > -- > > 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] Dihedral angle parameters in Gromacs and Amber
*Dear Gromacs society,* *I don't know how Gromacs define and calculate the multiplicity and equilibrium dihedral angle? For example, in Amber, the multiplicity is 1 and -3 but in Gromacs it is 1 and 3; All phi0 values in gromacs are positive but they are negative in Amber.* *Thank you very much in advance.* *Best regards,* *Lan Hoa* -- 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] Exchange temperature instead of exchange coordinate in replica exchange molecular dynamics?
Hi all, I am reading the paper "Replica-exchange molecular dynamics method for protein folding" by Yuko Okamoto. In this paper, they exchange temperatures of 2 replica. To evaluate that replica exchange is successful, they calculate exchange probability; plot the temperature, potential energy per replica versue time. In Gromacs, coordinates of replica are exchanged instead. So besides evaluating exchange probability, how do I know that the replica exchange is sucessful? Since we exchange coordinate, one replica just stay at 1 temperature, so we will not see the result of the paper by Yuko, I mean, one replica actually visit all the temperature. How about potential energy, should I expect that one replica visit all range of potential energy when we exchange coordinates of replica? Also, is this bad if exchange probability too high, let's say 0.8? Thanks in advance. Best regards, *Lan Hoa* -- 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] Exclusion - determine neighboring atoms by atom indices or by bond connections?
Dear Gromacs community, In the Gromacs manual, if nrexcl = 3, that means atoms i+1, i+2, i+3 are excluded from non-bonded interactions with atom i. I don't know how Gromacs determine the neighboring atoms, based on atom indices or bond connections? For example, if I have a simple connection between CA and CB atoms like the following CA(1) -CA(3)---CA(5)CA(7) | | | | CB(2) CB(4)CB(6) CB(8) Indices of atoms are shown in the brackets. If the neighbouring atoms are determined based on atom indices, that means CB(2) will not form non-bonded interactions with CA(3), CB(4),CA(5) but still form non-bonded interactions with CA(1), that is what I don't want since CB(2) and CA(1) already form bonded interaction (harmonic bond energy) It really confused me. I am looking forward to hearing from you. Thank you very much in advance. Best regards, *Lan Hoa* -- 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] ATOMTYPES directive
Dear Gromacs community, In the [ atomtypes ] directive, according to Gromacs manual, it should have 7 seperated fields, which are name, at.num, mass, charge, ptype, c6, c12. However, when I remove the field of at.num, Gromacs still works without notifying any error. If I insert 2 fields more, it still doesn't notify error. Only when I insert 3 fields more, it start notifying error. I don't understand how Gromacs read through all the parameters and determine what is c6, c12, etc... I am looking forward to hearing from you. Thank you very much in advance. Best regards, *Lan Hoa* -- 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] How to define (or modify) a new potential function in Gromacs?
Dear Gromacs community, I am attemping to use Gromacs for a Coarse - grained simulation. In our model, we have a term similar to the angle harmonic potential term, but the variable is not angle but the volume created by three consecutive vectors. I don't know if there is a way to implement that kind of potential in Gromacs? I am looking forward to hearing from you. Thank you very much in advanced, Best regards, *Lan Hoa* -- 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] Equilibration at each temperature in simmulated annealing
Thanks! sorry for the spelling error, I just meant tcoupl. Sent from my iPhone > On Sep 26, 2017, at 6:30 AM, Mark Abraham wrote: > > Hi, > > It'll equilibrate if you leave it alone long enough at an annealing point, > as normal. See > http://manual.gromacs.org/documentation/2016.4/user-guide/mdp-options.html#simulated-annealing. > I don't know what you mean by referring to the non-existent t_couple > > Mark > >> On Tue, Sep 26, 2017 at 8:49 AM Hoa Trinh wrote: >> >> Hi all, >> I would like to cool my system from 200K to 100K via multiple intermediate >> temperatures and at each temperature, the system is equilibrated for a >> while before decreasing temperature. >> I am thinking of doing something like this: >> annealing_temp = 200 150 150 100 100 >> But I am afraid this is not going to equilibrate my system at 150K since I >> only have one value of t_couple in mdp file. That means I can only choose >> to equilibrate my system at either 150K or 100K. >> So how can I equilibrate my system at each temperature in simulated >> annealing? >> I am looking forward to hearing from you. >> Thanks in advance! >> Best regards, >> *Lan Hoa* >> -- >> 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.
