Re: [gmx-users] Regarding RMSD analysis result
Dear justin
http://rmsdnagasundaram.blogspot.in/. This is the link to
my rmsd graph. Plz check it once and suggest me.
Thanks
On Mon, Sep 24, 2012 at 10:10 PM, ahmet yıldırım ahmedo...@gmail.comwrote:
Dear Tsjerk,
You said RMSD's above 1 nm are suspect, towards 2 highly likely not
correct. What is the physical/biological/chemical meaning of what you say?
Greetings
2012/9/24 Tsjerk Wassenaar tsje...@gmail.com
Hi,
RMSD's above 1 nm are suspect, towards 2 highly likely not correct.
You have to make sure that the molecule is made whole before doing
RMSD analysis.
Cheers,
Tsjerk
On Mon, Sep 24, 2012 at 3:02 PM, lloyd riggs lloyd.ri...@gmx.ch wrote:
You can also just quickly visualize it in VMD and see if anything your
looking at is not centred properly. If it isnt you just have to centre
it.
Stephan
Original-Nachricht
Datum: Mon, 24 Sep 2012 04:32:33 -0700
Von: naga sundar naga25sun...@gmail.com
An: Discussion list for GROMACS users gmx-users@gromacs.org
Betreff: Re: [gmx-users] Regarding RMSD analysis result
Dear justin
Thanks for ur suggestions
While speaking about periodic conditions, I
followed
the similar condition for both native and mutant complexes. For native
complexes not any big deviation was observed. So its confirmed that
nothing
wrong with periodic conditions. Since all the three mutations were
having
high clinical significance, we assuming mutation is the only reason
for
this abnormal RMSD behavior. Sudden big increase in the RMSD was
observed
in previous mutational MD studies.
http://www.sciencedirect.com/science/article/pii/S0006291X08020792.
Overall, all the factors are supporting our results. So shall we take
this
RMSD analysis as good result . Even after repeating the 20 ns MD
simulation
two times i got the same results.
On Mon, Sep 24, 2012 at 3:41 AM, Justin Lemkul jalem...@vt.edu
wrote:
On 9/24/12 6:24 AM, naga sundar wrote:
Dear gromacs users
We performed MD simulation analysis for native and
mutant
models of protein-protein complexes. From 20 ns simulation
trajectory,
we
generated RMSD graph for one native and three mutant complexes. For
native
complex in the entire simulation period, we observed a constant
RMSD
(~0.15 to ~ 0.25 nm). But, three mutant complexes
showed drastic fluctuation in theRMSD (~0.15 to ~1.75) plot. We
analysed
all the 3D structure's in the fluctuated areas observed destruction
of
protein complexes.
All the three mutants were already experimentally analyzed and
reported
that they are involved in the destruction of protein-protein
interactions.
Query 1: What may be the reason for sudden rise and fall of the
RMSD
values
in mutant complexes. We are assume its because of the involvement
of
mutation.
Query 2: Is there may any other reasons for drastic fluctuation in
the
RMSD
Query 3: Observed results are rite.
Here iam attaching the RMSD graph for your observation.
Attachments to the list do not work. You will have to post a link
to
a
file sharing site if you wish to share an image.
Such jumps in RMSD are very suspect. Since you are dealing with
protein-protein complexes, accounting for periodicity can be very
challenging. Have you properly fit the trajectory such that your
protein
subunits are not jumping across periodic boundaries? If they are,
then
your results are nothing more than an artifact. If they are not,
then
you
have something more interesting, but a tenfold increase in RMSD is
very
peculiar.
-Justin
--
==**==
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
==**==
--
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Re: [gmx-users] Regarding RMSD analysis result
It looks for me like the known pbc effect others already pointed to. If you have just a protein-ligand complex (+ water and counterions of course) it's relatively easy to manually (a piece of code would do it) bring the ligand to the correct position in the frames showing an abnormally high value by subtracting half the x/y dimension of the box from its coordinates and re-calculate the rmsd , but I think trjconv would do it as well. Felipe On 09/25/2012 09:22 AM, naga sundar wrote: Dear justin http://rmsdnagasundaram.blogspot.in/. This is the link to my rmsd graph. Plz check it once and suggest me. Thanks -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Regarding RMSD analysis result
Dear Felipe Thanks for ur reply. The system is a protein-protein complex. Like u r saying its due to pbc problem then why any abnormality doesn't happened to the native complex (Black line)?. As already suggest by justin i checked the pbc conditions upto my knowledge everything is fine. of-course this is not the first MD run for these native and mutant complexes. I run twice and got the same results. I want know this kind of RMSD is rite r wrong?.. On Tue, Sep 25, 2012 at 12:45 AM, Felipe Pineda, PhD luis.pinedadecas...@lnu.se wrote: It looks for me like the known pbc effect others already pointed to. If you have just a protein-ligand complex (+ water and counterions of course) it's relatively easy to manually (a piece of code would do it) bring the ligand to the correct position in the frames showing an abnormally high value by subtracting half the x/y dimension of the box from its coordinates and re-calculate the rmsd , but I think trjconv would do it as well. Felipe On 09/25/2012 09:22 AM, naga sundar wrote: Dear justin http://rmsdnagasundaram.**blogspot.in/http://rmsdnagasundaram.blogspot.in/. This is the link to my rmsd graph. Plz check it once and suggest me. Thanks -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Regards N.NagaSundaram -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Regarding RMSD analysis result
On 09/25/2012 10:08 AM, naga sundar wrote: Dear Felipe Thanks for ur reply. The system is a protein-protein complex. Like u r saying its due to pbc problem then why any abnormality doesn't happened to the native complex (Black line)?. Maybe because MD is stochastic ... As already suggest by justin i checked the pbc conditions upto my knowledge everything is fine. As Justin said, it's not about the pbc conditions as they appear in the mdp file, but about pbc effects due to a chain, probably the ligand, leaving the box and being reflected to the opposite side. Have you checked out visually how the weird frames look like? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] adding mix solvent
On Tue, Sep 25, 2012 at 11:57 AM, Nur Syafiqah Abdul Ghani pqah...@gmail.com wrote: Dear All, I already produce my co-solvent topology file also with gro file. Next step is i need to put the co-solvent first before i enter the water molecule inside my box and mix them with the protein. But right now i had a problem during put the co-solvent part. I used this command : genbox -cp protein_box.gro -ci solv.gro -p control.top -o protein_solv.gro but then there was no any molecule of my co-solvent inside the box with the protein. Then i know i must have the itp file to include in the control topology. But what i can do with the topology of the co-solvent?What is the relationship between co-solvent.gro and co-solvent.top which i might can used both of them in my GROMACS simulation? Four your infomation i used antechamber to produced my co-solvent topology. Any advises from the pro one? Thanks in advance! -- Best Regards, Nur Syafiqah Abdul Ghani, Theoretical and Computational Chemistry Laboratory, Department of Chemistry, Faculty of Science, Universiti Putra Malaysia, 43400 Serdang, Selangor. 013-7188131 alternative email : syafiqahabdulgh...@gmail.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists Dear user you need to determine the number of co-solvent molecule in genbox command with -nmol option. -- masumeh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Regarding RMSD analysis result
Hi, Your RMSD graph is ok but is represented wrong due to pbc problem. Use whole and nojump options of trjconv. On Tue, Sep 25, 2012 at 2:15 PM, Felipe Pineda, PhD luis.pinedadecas...@lnu.se wrote: On 09/25/2012 10:08 AM, naga sundar wrote: Dear Felipe Thanks for ur reply. The system is a protein-protein complex. Like u r saying its due to pbc problem then why any abnormality doesn't happened to the native complex (Black line)?. Maybe because MD is stochastic ... As already suggest by justin i checked the pbc conditions upto my knowledge everything is fine. As Justin said, it's not about the pbc conditions as they appear in the mdp file, but about pbc effects due to a chain, probably the ligand, leaving the box and being reflected to the opposite side. Have you checked out visually how the weird frames look like? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Regarding RMSD analysis result
Hi, trjconv -s top.tpr -f traj.xtc -o traj-nojump.xtc -pbc nojump I hope it helps 2012/9/25 Archana Sonawani ask.arch...@gmail.com Hi, Your RMSD graph is ok but is represented wrong due to pbc problem. Use whole and nojump options of trjconv. On Tue, Sep 25, 2012 at 2:15 PM, Felipe Pineda, PhD luis.pinedadecas...@lnu.se wrote: On 09/25/2012 10:08 AM, naga sundar wrote: Dear Felipe Thanks for ur reply. The system is a protein-protein complex. Like u r saying its due to pbc problem then why any abnormality doesn't happened to the native complex (Black line)?. Maybe because MD is stochastic ... As already suggest by justin i checked the pbc conditions upto my knowledge everything is fine. As Justin said, it's not about the pbc conditions as they appear in the mdp file, but about pbc effects due to a chain, probably the ligand, leaving the box and being reflected to the opposite side. Have you checked out visually how the weird frames look like? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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/**Support/Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- Ahmet Yıldırım -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] elastic network model - atoms movement
Hi all, I want to build elastic network model using gromacs. I consider only c-alpha atoms and only bond stretching term contributes to towards potential energy. Bonds are connected between atoms present with in certain cut-off distance(modified topology accordingly). When I run md the atoms are not present at the equillibrium distance but moving very far distances , in different directions. I do not want to use constraints. How can i avoid this? 2) Has anyone built elastic network model in gromacs? Please suggest me a way, Thank you in advance, Mohan. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Reference for CHARMM36 Force Field Conversion
Hi everyone, This message is just to let people know that there is finally a reference that we ask you to cite if you publish work using the CHARMM36 lipid force field contribution available from the GROMACS website. The reference is provided in a new version of the forcefield.doc file, and is also given below: Thomas J. Piggot, Ángel Piñeiro and Syma Khalid Molecular Dynamics Simulations of Phosphatidylcholine Membranes: A Comparative Force Field Study Journal of Chemical Theory and Computation DOI: 10.1021/ct3003157 http://pubs.acs.org/doi/abs/10.1021/ct3003157 A validation of the conversion for DPPC and POPC membrane systems (in terms of single point energies calculated in both GROMACS and NAMD) is provided in the supporting information of this work. Cheers Tom -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Error in domain decomposition
Hi, I am a newbie in Gromacs and is trying to simulate a small organic molecule in water. I got the following error message during a position restrained md run. I tried changing number of nodes but without success. Any help on this is appreciated. Initializing Domain Decomposition on 16 nodes Dynamic load balancing: auto Will sort the charge groups at every domain (re)decomposition Initial maximum inter charge-group distances: two-body bonded interactions: 0.400 nm, LJ-14, atoms 10 14 multi-body bonded interactions: 0.400 nm, Ryckaert-Bell., atoms 10 14 Minimum cell size due to bonded interactions: 0.440 nm Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.761 nm Estimated maximum distance required for P-LINCS: 0.761 nm This distance will limit the DD cell size, you can override this with -rcon Guess for relative PME load: 0.21 Will use 12 particle-particle and 4 PME only nodes This is a guess, check the performance at the end of the log file Using 4 separate PME nodes Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25 Optimizing the DD grid for 12 cells with a minimum initial size of 0.951 nm The maximum allowed number of cells is: X 2 Y 2 Z 2 --- Program mdrun_mpi_d, VERSION 4.5.5 Source code file: domdec.c, line: 6436 Fatal error: There is no domain decomposition for 12 nodes that is compatible with the given box and a minimum cell size of 0.95125 nm Change the number of nodes or mdrun option -rcon or -dds or your LINCS settings Look in the log file for details on the domain decomposition For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- -best, Dipankar Roy -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Error in domain decomposition
On 9/25/12 12:20 PM, Dipankar Roy wrote: Hi, I am a newbie in Gromacs and is trying to simulate a small organic molecule in water. I got the following error message during a position restrained md run. I tried changing number of nodes but without success. Any help on this is appreciated. Initializing Domain Decomposition on 16 nodes Dynamic load balancing: auto Will sort the charge groups at every domain (re)decomposition Initial maximum inter charge-group distances: two-body bonded interactions: 0.400 nm, LJ-14, atoms 10 14 multi-body bonded interactions: 0.400 nm, Ryckaert-Bell., atoms 10 14 Minimum cell size due to bonded interactions: 0.440 nm Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.761 nm Estimated maximum distance required for P-LINCS: 0.761 nm This distance will limit the DD cell size, you can override this with -rcon Guess for relative PME load: 0.21 Will use 12 particle-particle and 4 PME only nodes This is a guess, check the performance at the end of the log file Using 4 separate PME nodes Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25 Optimizing the DD grid for 12 cells with a minimum initial size of 0.951 nm The maximum allowed number of cells is: X 2 Y 2 Z 2 --- Program mdrun_mpi_d, VERSION 4.5.5 Source code file: domdec.c, line: 6436 Fatal error: There is no domain decomposition for 12 nodes that is compatible with the given box and a minimum cell size of 0.95125 nm Change the number of nodes or mdrun option -rcon or -dds or your LINCS settings Look in the log file for details on the domain decomposition For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Did you follow the link and read the following information? http://www.gromacs.org/Documentation/Errors#There_is_no_domain_decomposition_for_n_nodes_that_is_compatible_with_the_given_box_and_a_minimum_cell_size_of_x_nm Depending on the size of your system it may not be practical (or even possible) to decompose it into more than one or two cells. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] i can not simulate box of water,
On 9/25/12 11:15 AM, Ali Alizadeh wrote: Dear All users I made a box of water molecules(w.pdb to w.gro by pdb2gmx then i used genbox for made a box), but the grompp did not identify molecules(water mode SPC), error: atom 5721 in wbox.top does not match with in wbox.gro atom 5722 in ..., . . . These do not look like the actual error messages. Please copy and paste from the terminal rather than retyping and paraphrasing. Likely the atoms are out of order with respect to the topology and you're getting name mismatches, but this should not be the case if pdb2gmx produced the coordinate file. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] error with x2top.
Dear all, i am trying to convert a .gro file into a top file using .x2top but not all atoms can be assigned forcefields and the code stops with the error: Generating bonds from distances...atom 94Can not find forcefield for atom C-2 with 2 bondsCan not find forcefield for atom S-3 with 0 bondsCan not find forcefield for atom C-4 with 2 bondsCan not find forcefield for atom C-7 with 3 bondsCan not find forcefield for atom C-10 with 3 bondsCan not find forcefield for atom S-12 with 0 bondsCan not find forcefield for atom C-13 with 2 bondsCan not find forcefield for atom C-16 with 2 bondsCan not find forcefield for atom O-17 with 2 bondsCan not find forcefield for atom O-18 withFatal error:Could only find a forcefield type for 73 out of 94 atoms I looked at the .atp and n2t files. I am not sure where to start. is the second column partial charges? how to determine these? are they automatically determined ..what about the numbers at the end after each atom symbol? Is there any clear examples of how to do this? Any help would be appreciated. Thanks Elie -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] error with x2top.
On 9/25/12 4:28 PM, Elie M wrote: Dear all, i am trying to convert a .gro file into a top file using .x2top but not all atoms can be assigned forcefields and the code stops with the error: Generating bonds from distances...atom 94Can not find forcefield for atom C-2 with 2 bondsCan not find forcefield for atom S-3 with 0 bondsCan not find forcefield for atom C-4 with 2 bondsCan not find forcefield for atom C-7 with 3 bondsCan not find forcefield for atom C-10 with 3 bondsCan not find forcefield for atom S-12 with 0 bondsCan not find forcefield for atom C-13 with 2 bondsCan not find forcefield for atom C-16 with 2 bondsCan not find forcefield for atom O-17 with 2 bondsCan not find forcefield for atom O-18 withFatal error:Could only find a forcefield type for 73 out of 94 atoms I looked at the .atp and n2t files. I am not sure where to start. is the second column partial charges? how to determine these? are they automatically determined ..what about the numbers at the end after each atom symbol? Is there any clear examples of how to do this? Any help would be appreciated. Thanks The format is explained in full here: http://www.gromacs.org/Documentation/File_Formats/.n2t_File The charges and atom types are determined by parameterizing the molecule of interest, but if you're going to do that much work, it's probably simpler to create an .rtp entry and have pdb2gmx do the work. g_x2top is usually intended to create simple topologies for simple molecules. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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/Support/Mailing_Lists/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/Support/Mailing_Lists
RE: [gmx-users] error with x2top.
Thanks for your reply. I guess either way (x2top or pdb2gmx), I have problems. pdb2gmx is giving the same old error residue 'UNK' is not found in topology residue file whereas strangely enough x2top did not complain and was able to assign topologies for 73 atoms out of 94 so maybe it is easier to use x2top because in the other case I have to change files and I have no experience in this whatsoever and I am really tight on time. What do you personally think? Regards Date: Tue, 25 Sep 2012 16:32:33 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] error with x2top. On 9/25/12 4:28 PM, Elie M wrote: Dear all, i am trying to convert a .gro file into a top file using .x2top but not all atoms can be assigned forcefields and the code stops with the error: Generating bonds from distances...atom 94Can not find forcefield for atom C-2 with 2 bondsCan not find forcefield for atom S-3 with 0 bondsCan not find forcefield for atom C-4 with 2 bondsCan not find forcefield for atom C-7 with 3 bondsCan not find forcefield for atom C-10 with 3 bondsCan not find forcefield for atom S-12 with 0 bondsCan not find forcefield for atom C-13 with 2 bondsCan not find forcefield for atom C-16 with 2 bondsCan not find forcefield for atom O-17 with 2 bondsCan not find forcefield for atom O-18 withFatal error:Could only find a forcefield type for 73 out of 94 atoms I looked at the .atp and n2t files. I am not sure where to start. is the second column partial charges? how to determine these? are they automatically determined ..what about the numbers at the end after each atom symbol? Is there any clear examples of how to do this? Any help would be appreciated. Thanks The format is explained in full here: http://www.gromacs.org/Documentation/File_Formats/.n2t_File The charges and atom types are determined by parameterizing the molecule of interest, but if you're going to do that much work, it's probably simpler to create an .rtp entry and have pdb2gmx do the work. g_x2top is usually intended to create simple topologies for simple molecules. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] error with x2top.
On 9/25/12 5:02 PM, Elie M wrote: Thanks for your reply. I guess either way (x2top or pdb2gmx), I have problems. pdb2gmx is giving the same old error residue 'UNK' is not found in topology residue file whereas strangely enough x2top did not complain and was able to assign topologies for 73 atoms out of 94 so maybe it is easier to use x2top because in the other case I have to change files and I have no experience in this whatsoever and I am really tight on time. What do you personally think? Neither tool is guaranteed to produce a topology for an arbitrary molecule. If g_x2top does not have the right parameters, it will fail. If pdb2gmx does not have the right parameters, it will fail. g_x2top further assumes that some generic set of atom types and functional groups will address whatever it is that you're working with. Sometimes that's appropriate, sometimes it's not. Either way, you're going to have to modify either the .n2t file or the .rtp file for your chosen force field. Regardless of the route you choose, you're going to have to come up with parameters for your molecule and learn how these files work so you can modify them. Parameterization is an expert topic for a reason. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Restrain specific lipid residues
Hi everyone, This is probably a very silly question, but if I want to restrain only certain lipid residues in my bilayer, based on their residue number, is there some other way to do this aside from just having an explicit residue-by-residue list of them their topologies in my .top? I'm just using Tieleman's lipid parameters, so I cannot define the lipid residues to restrain following the popc.itp file, since it describes just the general topology for any POPC residue tells me that my index is out of range, since the .top is in atom numbers I'm trying to think in residue numbers. Does that sort of make sense? Out of my 165 residues, I want to strongly restrain only 33 of them, and then let the rest minimize (I'm trying to add onto an equilibrated box - at this point, it would have just been easier to start over from scratch, but I thought I would ask). Also, thank you to Justin and Mark for your help with hydrogen building in pdb2gmx - you were right, obviously, I was just not noticing the wrong atom type in my .h2b file (way back Aug 30th). Thank you for your help, Katrina-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
RE: [gmx-users] error with x2top.
Yep You are right. I will try my best to change the files accordingly. Thanks Date: Tue, 25 Sep 2012 17:05:20 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] error with x2top. On 9/25/12 5:02 PM, Elie M wrote: Thanks for your reply. I guess either way (x2top or pdb2gmx), I have problems. pdb2gmx is giving the same old error residue 'UNK' is not found in topology residue file whereas strangely enough x2top did not complain and was able to assign topologies for 73 atoms out of 94 so maybe it is easier to use x2top because in the other case I have to change files and I have no experience in this whatsoever and I am really tight on time. What do you personally think? Neither tool is guaranteed to produce a topology for an arbitrary molecule. If g_x2top does not have the right parameters, it will fail. If pdb2gmx does not have the right parameters, it will fail. g_x2top further assumes that some generic set of atom types and functional groups will address whatever it is that you're working with. Sometimes that's appropriate, sometimes it's not. Either way, you're going to have to modify either the .n2t file or the .rtp file for your chosen force field. Regardless of the route you choose, you're going to have to come up with parameters for your molecule and learn how these files work so you can modify them. Parameterization is an expert topic for a reason. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Restrain specific lipid residues
On 9/25/12 5:14 PM, Katrina Lexa wrote: Hi everyone, This is probably a very silly question, but if I want to restrain only certain lipid residues in my bilayer, based on their residue number, is there some other way to do this aside from just having an explicit residue-by-residue list of them their topologies in my .top? I'm just using Tieleman's lipid parameters, so I cannot define the lipid residues to restrain following the popc.itp file, since it describes just the general topology for any POPC residue tells me that my index is out of range, since the .top is in atom numbers I'm trying to think in residue numbers. Does that sort of make sense? Out of my 165 residues, I want to strongly restrain only 33 of them, and then let the rest minimize (I'm trying to add onto an equilibrated box - at this point, it would have just been easier to start over from scratch, but I thought I would ask). Restraints can only be applied per [molecultype], so no, there is no way to have a global lipid topology and individual restraint files for individual molecules. It is possible to reduce the complexity a bit by defining the 33 restrained lipids as one [moleculetype], though they would have to be consecutive in your coordinate file as well, which may require manual reorganization. Also, thank you to Justin and Mark for your help with hydrogen building in pdb2gmx - you were right, obviously, I was just not noticing the wrong atom type in my .h2b file (way back Aug 30th). Glad to hear there's at least one problem solved :) -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Installation in a SGI Cluster
Check to see if the MPICC and MPI_HOME environment variables are set correctly to configure (it can't find mpicc). On 2012-09-25 12:06:14PM -0300, Diego Nolasco wrote: Hello GROMACS users, I am facing some problems to configure the gromacs installation in a x86_64 GNU/Linux SGI Cluster XE with Suse. I am using ./configure --enable-mpi --without-x --disable-float and the error comes as below: checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking how to create a ustar tar archive... gnutar checking for cc... cc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether cc accepts -g... yes checking for cc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of cc... gcc3 checking dependency style of cc... gcc3 checking for mpxlc... no checking for mpicc... no checking for mpcc... no checking for hcc... no checking whether the MPI cc command works... configure: error: Cannot compile and link MPI code with cc I would really appreciate if someone assist me in this regard. Thank's in advance, Diego Nolasco. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics Div. of Research | 705 South 20th Street p...@uab.edu| Birmingham AL 35294-4461 (205) 690-0808 | == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] a quick question (forgot to ask).
Sorry one more thing: For one of the atoms S that x2top did not assign the topology it said 0 bonds although S is a part of the Thiophene molecule which is connected to two carbons..what does it mean 0 bonds? Thanks From: elie.mouj...@hotmail.co.uk To: gmx-users@gromacs.org Subject: RE: [gmx-users] error with x2top. Date: Tue, 25 Sep 2012 22:17:21 +0100 Yep You are right. I will try my best to change the files accordingly. Thanks Date: Tue, 25 Sep 2012 17:05:20 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] error with x2top. On 9/25/12 5:02 PM, Elie M wrote: Thanks for your reply. I guess either way (x2top or pdb2gmx), I have problems. pdb2gmx is giving the same old error residue 'UNK' is not found in topology residue file whereas strangely enough x2top did not complain and was able to assign topologies for 73 atoms out of 94 so maybe it is easier to use x2top because in the other case I have to change files and I have no experience in this whatsoever and I am really tight on time. What do you personally think? Neither tool is guaranteed to produce a topology for an arbitrary molecule. If g_x2top does not have the right parameters, it will fail. If pdb2gmx does not have the right parameters, it will fail. g_x2top further assumes that some generic set of atom types and functional groups will address whatever it is that you're working with. Sometimes that's appropriate, sometimes it's not. Either way, you're going to have to modify either the .n2t file or the .rtp file for your chosen force field. Regardless of the route you choose, you're going to have to come up with parameters for your molecule and learn how these files work so you can modify them. Parameterization is an expert topic for a reason. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] a quick question (forgot to ask).
On 9/25/12 5:20 PM, Elie M wrote: Sorry one more thing: For one of the atoms S that x2top did not assign the topology it said 0 bonds although S is a part of the Thiophene molecule which is connected to two carbons..what does it mean 0 bonds? It means there is no entry in the .n2t file that matches this atom. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Restrain specific lipid residues
That's a simple enough way to deal with it - thanks! On Sep 25, 2012, at 2:16 PM, Justin Lemkul wrote: On 9/25/12 5:14 PM, Katrina Lexa wrote: Hi everyone, This is probably a very silly question, but if I want to restrain only certain lipid residues in my bilayer, based on their residue number, is there some other way to do this aside from just having an explicit residue-by-residue list of them their topologies in my .top? I'm just using Tieleman's lipid parameters, so I cannot define the lipid residues to restrain following the popc.itp file, since it describes just the general topology for any POPC residue tells me that my index is out of range, since the .top is in atom numbers I'm trying to think in residue numbers. Does that sort of make sense? Out of my 165 residues, I want to strongly restrain only 33 of them, and then let the rest minimize (I'm trying to add onto an equilibrated box - at this point, it would have just been easier to start over from scratch, but I thought I would ask). Restraints can only be applied per [molecultype], so no, there is no way to have a global lipid topology and individual restraint files for individual molecules. It is possible to reduce the complexity a bit by defining the 33 restrained lipids as one [moleculetype], though they would have to be consecutive in your coordinate file as well, which may require manual reorganization. Also, thank you to Justin and Mark for your help with hydrogen building in pdb2gmx - you were right, obviously, I was just not noticing the wrong atom type in my .h2b file (way back Aug 30th). Glad to hear there's at least one problem solved :) -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Deuterium and the meaning of the atomic number parameter
Hi, In my system, I have several hydroxyl groups. I would like to change the hydroxyl hydrogens to deuterium (as an approximation, I will just double the typical hydrogen mass). I am only doing this as a test of the dependance on mass of my system, so while I am sure force fields involving deuterium exist in the literature, I will not be using them. My question is, if I am simply doubling the mass of my hydroxyl hydrogens, what atomic number should I use in my ffnonbonded.itp file? 1 or 2? (Since the mass of each atom is always specified in the topology, it is not clear to me what the atomic number parameter does in Gromacs.) Section 5.3.2 of the manual shows how the atomic number (at.num in the [ atomtypes ] directive) is specified in ffnonbonded.itp, but it is not clear to me what the atomic number actually does in Gromacs. From general chemistry, I know that the atomic number is simply the number of protons in the nucleus. Deuterium's nucleus consists of one proton and one neutron, so the atomic number of deuterium should be 1. Am I correct in setting the atomic number of deuterium as 1? Then my ffnonbonded.itp file will look like: [ atomtypes ] ;name at.num masscharge ptype sigma epsilon HO 1 2.01580 0.418 A ; sigma, epsilon Thank you for your time! Andrew DeYoung Carnegie Mellon University -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Deuterium and the meaning of the atomic number parameter
On 9/25/12 5:42 PM, Andrew DeYoung wrote: Hi, In my system, I have several hydroxyl groups. I would like to change the hydroxyl hydrogens to deuterium (as an approximation, I will just double the typical hydrogen mass). I am only doing this as a test of the dependance on mass of my system, so while I am sure force fields involving deuterium exist in the literature, I will not be using them. My question is, if I am simply doubling the mass of my hydroxyl hydrogens, what atomic number should I use in my ffnonbonded.itp file? 1 or 2? It would be 1. (Since the mass of each atom is always specified in the topology, it is not clear to me what the atomic number parameter does in Gromacs.) Section 5.3.2 of the manual shows how the atomic number (at.num in the [ atomtypes ] directive) is specified in ffnonbonded.itp, but it is not clear to me what the atomic number actually does in Gromacs. It does nothing. From general chemistry, I know that the atomic number is simply the number of protons in the nucleus. Deuterium's nucleus consists of one proton and one neutron, so the atomic number of deuterium should be 1. Am I correct in setting the atomic number of deuterium as 1? Then my ffnonbonded.itp file will look like: [ atomtypes ] ;name at.num masscharge ptype sigma epsilon HO 1 2.01580 0.418 A ; sigma, epsilon Correct (given the caveats you list above), so at the very least, syntactically correct. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Turning off charges of a particular atom type
Hi, If you have time, I have one more question. Suppose that I have some atom type named XX. Normally XX has a partial charge, but for a test simulation, I would like to turn off the charges of all of the XX atoms. This way, I will hopefully be able to disentangle the relative effects of Coulomb interactions (i.e., charges) and van der Waals/Lennard-Jones interactions in my system. Is it true that to turn off the charges of the XX atoms, I can simply set the charge parameter in my nonbonded topology (e.g., ffnonbonded.itp) to 0? Or is there a better way to do this? Thanks again so much for your time. Andrew DeYoung Carnegie Mellon University -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Turning off charges of a particular atom type
On 9/25/12 5:54 PM, Andrew DeYoung wrote: Hi, If you have time, I have one more question. Suppose that I have some atom type named XX. Normally XX has a partial charge, but for a test simulation, I would like to turn off the charges of all of the XX atoms. This way, I will hopefully be able to disentangle the relative effects of Coulomb interactions (i.e., charges) and van der Waals/Lennard-Jones interactions in my system. Is it true that to turn off the charges of the XX atoms, I can simply set the charge parameter in my nonbonded topology (e.g., ffnonbonded.itp) to 0? Or is there a better way to do this? Charges in ffnonbonded.itp are not used. You would have to zero out the charges in the topology (.top or .itp). -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Re: Turning off charges of a particular atom type
Justin, Thank you for the reminder! I can't believe I forgot that important fact about ffnonbonded.itp, but I did. Andrew DeYoung Carnegie Mellon University -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
