Re: Re[4]: [gmx-users] Non-conservation of total energy while using structure file to resume the simulation
Hi Dmitri, Try editconf -f your_run_input_file.tpr -o test.gro to see if the box is stored correctly in the .tpr. Alternatively, you can do gmxdump -s your_run_input_file.tpr, and browse for the box in the output. Then, see if you can reproduce the problem with the last frame of the .trr file extracted, and consider submitting a bugzilla. Cheers, Tsjerk On Wed, Jun 9, 2010 at 8:54 AM, Dmitri Dubov wrote: > First, sorry for the revival of this thread so late (maybe it should be > better to start a new one). > >> - Original Message - > >> From: Dmitri Dubov > >> Date: Thursday, May 27, 2010 19:11 > >> Subject: Re[2]: [gmx-users] Non-conservation of total energy while > >> using structure file to resume the simulation > >> To: Discussion list for GROMACS users > >>> > I expect that either > >>> > grompp -f new -o newtpr > >>> > mdrun -s newtpr -cpi old_state.cpt > >>> No, this way is unsuccessful, maybe due to somewhat contradictive >>> instructions: > >>> grompp supplies newtpr with usual options > >>> tinit = 0 > >>> nsteps = 10 > >>> simulation_part = 1 > >>> and from old_state.cpt the system finds itself on 10th step already >>> and stops. > >> OK. Presumably some more cunning choice of .mdp options would work, > >> or using grompp, tbconv -extend and then mdrun. > >>> > grompp -f new -t old_state.cpt -o newtpr > >>> > mdrun -s newtpr > >>> > will do what you want. Please report back if one or both work :-) > >>> And the latter variant is working! More precisely I use > >>> grompp -f new -t old_state.cpt -c oldtpr -o newtpr > >>> mdrun_d -s newtpr > >> Mark > > But I have noted just now that using grompp with -t option results in some > bug: after simulation right size of my cubic box (last line of input > structure file) > > 10.0 10.0 10.0 > > changes in confout.gro to meaningless > > 0.0 0.0 0.0 > > To analyse the output properly (e.g. with g_rdf tool) I have to correct this > line manually. > > And I'm worried whether this bug effects to my simulation itself, during md > integration of NVE ensemble in vacuum? > > -- > > Rerards, > > Dmitri mailto:ddu...@ngs.ru > > -- > gmx-users mailing list gmx-us...@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology University of Groningen The Netherlands -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: Simulation with CsCl
Hello All , I am also trying to simulate my protein with Mn ion present in it. So can I create the topology entry for Mn ion similar to MG2+ ion ? and how can I get the values of C6 and C12 leonard jones potential in [atom type] entry and will it be required to add [nonbond_params] also ? how can I get them ? Also I want to use Fe2+ also, but it is also not included in gromos force field. This problem of adding other ions and molecule in the system always remains. And being new to this field, can someone suggest in simple terms how to include these considering the person is not an expert in this field. Please help. -- Sonali Dhindwal --- On Tue, 8/6/10, Vitaly Chaban wrote: From: Vitaly Chaban Subject: [gmx-users] Re: Simulation with CsCl To: gmx-users@gromacs.org Date: Tuesday, 8 June, 2010, 9:03 PM > Hi all: > I am trying to simulate a polysaccharide in solution of water and CsCl, but > cesium is not parametrized in the gromacs 4. I am using the force > field GROMOS 96. > I have looked for the parameters of Cs+ in the OPLS Force field and I have > created 4 files: Cs.atp, Cs.itp, Csnb.itp and Cs.rtp. Also I have include > the parameters for Cs+ in the "ions.itp" file, but it didn't work, Can > someone help me? > Thanks in advance. > Cecilia. Cecilia - You do not need so many files so cesium. Just copy your parameters to the force field used and create the topology entry for cesium similar to [ moleculetype ] Ar 1 [ atoms ] 1 Ar 1 Ar Ar 0 0.0 Do not forget, cesium+ is an ion... -- Dr. Vitaly Chaban -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] tracking the time for an md run
Hi, Can anyone let me know how to know how long the md run would take, or how long is left. I tried tailing it, but couldn't find a time factor there Thanks Rabab -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re[6]: [gmx-users] Non-conservation of total energy while using structure file to resume the simulation
Hi, Tsjerk. Thanks for your help. > Try > editconf -f your_run_input_file.tpr -o test.gro > to see if the box is stored correctly in the .tpr. Alternatively, you > can do gmxdump -s your_run_input_file.tpr, and browse for the box in > the output. Yea, both tests show "zero" box right in .tpr file! > Then, see if you can reproduce the problem with the last > frame of the .trr file extracted, I'm afraid I cannot do it quickly... For the future: I used double-precision mode, how much should be the precision (-ndec) of the extracted frame? > and consider submitting a bugzilla. Sure. > Cheers, > Tsjerk > On Wed, Jun 9, 2010 at 8:54 AM, Dmitri Dubov wrote: >> First, sorry for the revival of this thread so late (maybe it should be >> better to start a new one). >>> - Original Message - >>> From: Dmitri Dubov >>> Date: Thursday, May 27, 2010 19:11 >>> Subject: Re[2]: [gmx-users] Non-conservation of total energy while >>> using structure file to resume the simulation >>> To: Discussion list for GROMACS users > I expect that either > grompp -f new -o newtpr > mdrun -s newtpr -cpi old_state.cpt No, this way is unsuccessful, maybe due to somewhat contradictive instructions: grompp supplies newtpr with usual options tinit= 0 nsteps = 10 simulation_part = 1 and from old_state.cpt the system finds itself on 10th step already and stops. >>> OK. Presumably some more cunning choice of .mdp options would work, >>> or using grompp, tbconv -extend and then mdrun. > grompp -f new -t old_state.cpt -o newtpr > mdrun -s newtpr > will do what you want. Please report back if one or both work :-) And the latter variant is working! More precisely I use grompp -f new -t old_state.cpt -c oldtpr -o newtpr mdrun_d -s newtpr >>> Mark >> But I have noted just now that using grompp with -t option results in some >> bug: after simulation right size of my cubic box (last line of input >> structure file) >> 10.0 10.0 10.0 >> changes in confout.gro to meaningless >>0.0 0.0 0.0 >> To analyse the output properly (e.g. with g_rdf tool) I have to correct this >> line manually. >> And I'm worried whether this bug effects to my simulation itself, during md >> integration of NVE ensemble in vacuum? -- Regards, Dmitri -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] field-specified name for sulfate
Hi All I am trying to add sodium sulfate to the system but I receive this fetal error Fatal error: No such moleculetype SO4 Could anybody tell me what is the force field-specified name of sulfate ion in OPLS-AA/L all-atom force field? regards, Shiva -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] tracking the time for an md run
Rabab Toubar wrote: Hi, Can anyone let me know how to know how long the md run would take, or how long is left. I tried tailing it, but couldn't find a time factor there If you use mdrun -v, it will print a completion estimate as it goes along. -Justin Thanks Rabab -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: Simulation with CsCl
sonali dhindwal wrote: Hello All , I am also trying to simulate my protein with Mn ion present in it. So can I create the topology entry for Mn ion similar to MG2+ ion ? and how can I get the values of C6 and C12 leonard jones potential in [atom type] entry and will it be required to add [nonbond_params] also ? how can I get them ? Also I want to use Fe2+ also, but it is also not included in gromos force field. This problem of adding other ions and molecule in the system always remains. And being new to this field, can someone suggest in simple terms how to include these considering the person is not an expert in this field. Please consult the link I posted yesterday... http://www.gromacs.org/Documentation/How-tos/Parameterization What you're trying to do is far from trivial. Understand that parameterization, especially for transition metals, is very challenging, and standard molecular mechanics treatment of such species suffers from many limitations, which may or may not influence your results. -Justin Please help. -- Sonali Dhindwal --- On *Tue, 8/6/10, Vitaly Chaban //* wrote: From: Vitaly Chaban Subject: [gmx-users] Re: Simulation with CsCl To: gmx-users@gromacs.org Date: Tuesday, 8 June, 2010, 9:03 PM > Hi all: > I am trying to simulate a polysaccharide in solution of water and CsCl, but > cesium is not parametrized in the gromacs 4. I am using the force > field GROMOS 96. > I have looked for the parameters of Cs+ in the OPLS Force field and I have > created 4 files: Cs.atp, Cs.itp, Csnb.itp and Cs.rtp. Also I have include > the parameters for Cs+ in the "ions.itp" file, but it didn't work, Can > someone help me? > Thanks in advance. > Cecilia. Cecilia - You do not need so many files so cesium. Just copy your parameters to the force field used and create the topology entry for cesium similar to [ moleculetype ] Ar 1 [ atoms ] 1 Ar1Ar Ar0 0.0 Do not forget, cesium+ is an ion... -- Dr. Vitaly Chaban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org . Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: Simulation with CsCl
Dear Sonali,
Unfortunately development of force-field parameters is difficult, and
even more so for bivalent ions and transition metals. This is certainly
not suitable as a project to begin with.
Having said that, a careful search in the literature will reveal that
many sets of parameters for metal ions do exist. Try to find a set that
works best with the water model that you're using or your particular
model, and carry out some simulations to validate that the results are
correct, reproducible and robust. The following references discuss some
aspects of simulations of ions and proteins:
@article{Project2006,
Author = {Project, E. and Friedman, R. and Nachliel, E. and Gutman, M.},
Title = {A Molecular Dynamics Study of the Effect of Ca{2+} Removal
on Calmodulin Structure},
Journal = {Biophys. J.},
Volume= {90},
Pages = {3842-3850},
Year = {2006}
}
@Article{Fyta2010,
author = "Fyta, M and Kalcher, I and Dzubiella, J and Vrbka, L and Netz,
R R",
title = {Ionic force field optimization based on single-ion and ion-pair
solvation properties},
journal = "J Chem Phys",
year = "2010",
volume = "132",
pages = "024911-024911"
}
Ran.
sonali dhindwal wrote:
> Hello All ,
> I am also trying to simulate my protein with Mn ion present in it.
> So can I create the topology entry for Mn ion similar to MG2+ ion ?
> and how can I get the values of C6 and C12 leonard jones potential in
> [atom type] entry and will it be required to add [nonbond_params] also
> ? how can I get them ?
>
> Also I want to use Fe2+ also, but it is also not included in gromos
> force field. This problem of adding other ions and molecule in the
> system always remains. And being new to this field, can someone
> suggest in simple terms how to include these considering the person is
> not an expert in this field.
> Please help.
>
> --
> Sonali Dhindwal
>
>
> --- On *Tue, 8/6/10, Vitaly Chaban //* wrote:
>
>
> From: Vitaly Chaban
> Subject: [gmx-users] Re: Simulation with CsCl
> To: gmx-users@gromacs.org
> Date: Tuesday, 8 June, 2010, 9:03 PM
>
> > Hi all:
> > I am trying to simulate a polysaccharide in solution of water
> and CsCl, but
> > cesium is not parametrized in the gromacs 4. I am using the force
> > field GROMOS 96.
> > I have looked for the parameters of Cs+ in the OPLS Force field
> and I have
> > created 4 files: Cs.atp, Cs.itp, Csnb.itp and Cs.rtp. Also I
> have include
> > the parameters for Cs+ in the "ions.itp" file, but it didn't
> work, Can
> > someone help me?
> > Thanks in advance.
> > Cecilia.
>
> Cecilia -
>
> You do not need so many files so cesium. Just copy your parameters to
> the force field used and create the topology entry for cesium similar
> to
>
> [ moleculetype ]
> Ar 1
>
> [ atoms ]
> 1 Ar1Ar Ar0 0.0
>
> Do not forget, cesium+ is an ion...
>
> --
> Dr. Vitaly Chaban
> --
> gmx-users mailing listgmx-users@gromacs.org
>
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before
> posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org
> .
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
--
--
Ran Friedman
Postdoctoral Fellow
Computational Structural Biology Group (A. Caflisch)
Department of Biochemistry
University of Zurich
Winterthurerstrasse 190
CH-8057 Zurich, Switzerland
Tel. +41-44-639
Email: r.fried...@bioc.uzh.ch
Skype: ran.friedman
--
--
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Re: [gmx-users] field-specified name for sulfate
shiva birgani wrote: Hi All I am trying to add sodium sulfate to the system but I receive this fetal error Fatal error: No such moleculetype SO4 Could anybody tell me what is the force field-specified name of sulfate ion in OPLS-AA/L all-atom force field? Rather than implicating nomenclature as the problem, most likely your topology itself is to blame: http://www.gromacs.org/Documentation/Errors#Fatal_error.3a_No_such_moleculetype_XXX -Justin regards, Shiva -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] converting amber parameter to OPLS
Dear all: I'm considering to convert the ATP/ADP parameters from amber (http://www.pharmacy.manchester.ac.uk/bryce/amber ) into OPLS format. My question is, have you guys done similar things? If so, can you give me some information on what kind of thing I should be aware of? Like the scaling factor (fudgeQQ) in OPLS and so on? Thank you very much, Bin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_dipoles, average not the same as from g_analyze
Dear gromacs users, I have following question: With the use of the g_dipoles tool I have analysed the average dipole moment using following command: g_dipoles -f *.trr -s *.tpr -n *.ndx -av average.xvg I think the option -av calculates the average of the dipole moment of the system I have chosen. Following output is given: x1 = time (ps) y1 = y2 = ^2 y3 = - ^2 ... I have taken the root of y2 (y2^(1/2)) to get and plotted that against x1. Mtot.xvg corresponds to the following quantities: x1 = time (ps) y1 = M_x y2 = M_y y3 = M_z y4 = M_tot I plotted M_tot against time and calculated the average by using g_analyze. Now I have following problem: My average value from g_analyze is not equal to the value of which I received from g_dipoles. The difference between the two values is at about 20 Debye. Could you tell me the reason why there exists a difference? Does g_dipoles calculate the average in another way than g_analyze? Thank you for your kind answer in advance. Best regards, Emanuel Peter -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_dipoles, average not the same as from g_analyze
Dear gromacs users, Sorry but my last email was not correct. I have following question: With the use of the g_dipoles tool I have analysed the average dipole moment using following command: g_dipoles -f *.trr -s *.tpr -n *.ndx -av average.xvg I think the option -av calculates the average of the dipole moment of the system I have chosen. Following output is given: x1 = time (ps) y1 = aver1 y2 = aver2**2 y3 = aver1 - aver2**2 ... I have taken the root of aver2 (y2^(1/2)) to get and plotted that against x1. Mtot.xvg corresponds to the following quantities: x1 = time (ps) y1 = M_x y2 = M_y y3 = M_z y4 = M_tot I plotted M_tot against time and calculated the average by using g_analyze. Now I have following problem: My average value from g_analyze is not equal to the value of which I received from g_dipoles. The difference between the two values is at about 20 Debye. Could you tell me the reason why there exists a difference? Does g_dipoles calculate the average in another way than g_analyze? Thank you for your kind answer in advance. Best regards, Emanuel Peter -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] structure file long chains
I dont know if the hdb file is correct. Actually I want to learn how it works. 1- Manual says the third columns are name of new H atoms (here, H1, H2). why are they not the same as those in rtp file (H11, H12). There is no H1 and H2 in rtp file ( http://lists.gromacs.org/pipermail/gmx-users/2009-March/040125.html ) Also the control atoms: for example for the frist row in Eth: H1 C1 C2 -C2 This means H1 is connected to C1. In manual I read the other two depend on the code selected. Can you please explain what is the logic behind the other two atoms (C2 and -C2 in the forst row for example) Eth 2 2 6 H1 C1 C2 -C2 2 6 H2 C2 C1 +C1 EthB2 3 4 H1 C1 C2 +C1 2 6 H2 C2 C1 +C1 EthE2 2 6 H1 C1 C2 -C2 3 4 H2 C2 C1 -C2 2- If I want to use these residues (Eth, EthB..) then I do not need to include H atoms in my pdb file? The reason I am asking this, is because if I make a long chain using any software, I see H atoms in pdb file. and the reason I am inclined to use these residues is that they are easier to work with... ATOM 1 C1 EthB1 1.000 1.540 0.000 ATOM 2 C2 EthB1 2.456 2.041 0.000 ATOM 3 C1 Eth 2 2.456 3.581 0.000 ATOM 4 C2 Eth 2 3.912 4.083 0.000 ATOM 5 C1 EthE3 3.912 5.623 0.000 ATOM 6 C2 EthE3 5.368 6.124 0.000 3- since I will have to work with very long polymer chains (1000 monomer units) what is the best approach or software to make such a chain. Some of the softwares do not do atmo numbering properly (or lack residues names) and I have to make a a lot of changes manually which is a nightmare for big chains. Thanks, Moeed -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] structure file long chains
Moeed wrote: I dont know if the hdb file is correct. Actually I want to learn how it works. The .hdb file works. I've used it :) Did you try it yourself with the examples posted? 1- Manual says the third columns are name of new H atoms (here, H1, H2). why are they not the same as those in rtp file (H11, H12). There is no H1 and H2 in rtp file (http://lists.gromacs.org/pipermail/gmx-users/2009-March/040125.html ) H1 and H2 are the base names. Since 2 of each are added, 1 and 2 get appended to these names -> H11, H12, H21, and H22. Also the control atoms: for example for the frist row in Eth: H1 C1 C2 -C2 This means H1 is connected to C1. In manual I read the other two depend on the code selected. Can you please explain what is the logic behind the other two atoms (C2 and -C2 in the forst row for example) Look at the amino acids for examples. The +/- convention means "previous" and "next" residue, respectively (like a peptide backbone). Eth 2 2 6 H1 C1 C2 -C2 2 6 H2 C2 C1 +C1 EthB2 3 4 H1 C1 C2 +C1 2 6 H2 C2 C1 +C1 EthE2 2 6 H1 C1 C2 -C2 3 4 H2 C2 C1 -C2 2- If I want to use these residues (Eth, EthB..) then I do not need to include H atoms in my pdb file? The reason I am asking this, is because Correct. That's the purpose of the .hdb file. if I make a long chain using any software, I see H atoms in pdb file. and the reason I am inclined to use these residues is that they are easier to work with... It's up to you what you use. If you can produce an all-atom structure, then you don't need to rely on the .hdb file to add hydrogens for you. If you generate only C atoms, then the .hdb file will add the necessary hydrogens. ATOM 1 C1 EthB1 1.000 1.540 0.000 ATOM 2 C2 EthB1 2.456 2.041 0.000 ATOM 3 C1 Eth 2 2.456 3.581 0.000 ATOM 4 C2 Eth 2 3.912 4.083 0.000 ATOM 5 C1 EthE3 3.912 5.623 0.000 ATOM 6 C2 EthE3 5.368 6.124 0.000 3- since I will have to work with very long polymer chains (1000 monomer units) what is the best approach or software to make such a chain. Some of the softwares do not do atmo numbering properly (or lack residues names) and I have to make a a lot of changes manually which is a nightmare for big chains. I don't have any suggestions beyond the link I posted already. Maybe someone who routinely deals with polymers can comment on this one. -Justin Thanks, Moeed -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_dipoles, average not the same as from g_analyze
Dear Emanuel, Please, check http://lists.gromacs.org/pipermail/gmx-users/2010-March/049316.html and Berk reply. I did never use -av (-a ?) option, maybe there is similar bug in average.xvg. Anyway last column of Mtot.xvg gives really correct norm of M_tot vector! Regards, Dmitri - > Dear gromacs users, > Sorry but my last email was not correct. > I have following question: > With the use of the g_dipoles tool I have analysed the average > dipole moment using following command: > g_dipoles -f *.trr -s *.tpr -n *.ndx -av average.xvg > I think the option -av calculates the average of the dipole moment of the > system I have chosen. > Following output is given: > x1 = time (ps) > y1 = aver1 > y2 = aver2**2 > y3 = aver1 - aver2**2 > ... > I have taken the root of aver2 (y2^(1/2)) to get and plotted that against x1. > Mtot.xvg corresponds to the following quantities: > x1 = time (ps) > y1 = M_x > y2 = M_y > y3 = M_z > y4 = M_tot > I plotted M_tot against time and calculated the average by using g_analyze. > Now I have following problem: > My average value from g_analyze is not equal to the value of which I > received from g_dipoles. > The difference between the two values is at about 20 Debye. > Could you tell me the reason why there exists a difference? > Does g_dipoles calculate the average in another way than g_analyze? > Thank you for your kind answer in advance. > Best regards, > Emanuel Peter-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] angle restraints
hello I want to add angle restraints in my itp file for a ligand. what is the proper way of inserting angle restraint in .itp file ? Is there any keywords I have to add to my .mdp file for angle restraints? I have searched the mail archieve, I found many things about adding dihedral angle restraints but I couldnot find anything about adding angle restrains. Please advice. Subarna Thakur -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
