Re: [gmx-users] Warning: Pressure scaling more than 1%.

Hi, Increasing the tau-p value in the parameter file should help. Regards, Pawan On Mon, May 11, 2009 at 11:06 AM, Zhanglin Ni wrote: > Dear all, > when I run position-restrained simulation (total 15000steps). when it > reached 740 steps > Step 741 Warning: Pressure scaling more than 1%. > >

Re: [gmx-users] Are Gromos 45a3 and GROMOS 53a6 compatible?

On May 11, 2009, at 6:18 AM, Chih-Ying Lin wrote: Hi GROMOS 45a3 force field GROMOS 53a6 force field Are they compatible? Probably not. They are two different parameterization generations. The 53a6 being more recent! Mixing them is probably not a good idea! They have been parameterized differ

Re: [gmx-users] Warning: Pressure scaling more than 1%.

Pawan Kumar wrote: Hi, Increasing the tau-p value in the parameter file should help. ... if the problem is that tau-p is too small. If the problem is with the model physics or the equilibration, then the above either won't work or might mask the problem. Mark __

[gmx-users] pull code problem

hello, I am trying to do a pulling simulation with gromacs 4.0.2 I added the following lines to the .mdp input file for grompp: ... pull = constraint pull_geometry = distance pull_dim = Y Y Y pull_nstxout = 10 pull_nstfout = 10

RE: [gmx-users] pull code problem

Hi, Do you have another line with "pull =" somewhere in your mdp file? PS You should switch to Gromacs 4.0.4, since it contains several small bug fixes for the pull code. Berk > Date: Mon, 11 May 2009 12:38:35 +0300 > From: neamtuand...@gmail.com > To: gmx-users@gromacs.org > Subject: [gmx-use

Re: [gmx-users] how to use atom2cg.awk

Dear Sir: In fact, I have modified the script as you said, but the CG strucrute produced is not different  in secondary strucure with native PDB structure: CG structure became a line strucrue! Please help me! Or give me a good script! Thank you very much! Best regards!    --- 09年5月11日，周一, J

[gmx-users] pull code problem

Hi Berk, thank you for the reply here is my mdp file: ; ; User aneamtu ; Joi, 7 mai - 2009 ; Input file ; title = Production_runs ;define = -DPOSRES -DPOSRES_CA2+_IONS ;constraints = all-bonds integrator =

RE: [gmx-users] pull code problem

Hi, Maybe there is an older grompp in your path. Type grompp -h to see which version you are using. And: which grompp to see where it comes from. Berk > Date: Mon, 11 May 2009 13:03:07 +0300 > From: neamtuand...@gmail.com > To: gmx-users@gromacs.org > Subject: [gmx-users] pull code problem > >

[gmx-users] pull code problem solved..

Sorry it appears that something was wrong with my .mdp file .. Idon't know what ...but I wrote again the pull code lines and the warnings dissapeared. Thank you again, Andrei ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mail

Re: [gmx-users] how to use atom2cg.awk

xi zhao wrote: Dear Sir: In fact, I have modified the script as you said, but the CG strucrute produced is not different in secondary strucure with native PDB structure: CG structure became a line strucrue! Please help me! Or give me a good script! Visualization is not an appropriate meth

[gmx-users] Re: reg Mopac/gromacs installations reply please

Please keep all correspondence on the gmx-users list. I do not have any further advice beyond what Mark already told you. Your shell environment is either severely broken, or your system too antiquated to work properly. IIRC, Red Hat 5 is from the late 1990's - you should definitely upgrade

Re: [gmx-users] how to use atom2cg.awk

Dear sir: This is my modified script, please see it! I take CG simulations  according to   http://md.chem.rug.nl/marrink/coarsegrain.html. Thank you ! --- 09年5月11日，周一, Justin A. Lemkul 写道： 发件人: Justin A. Lemkul 主题: Re: [gmx-users] how to use atom2cg.awk 收件人: "Gromacs Users' List" 日期: 20

Re: [gmx-users] how to use atom2cg.awk

xi zhao wrote: Dear sir: This is my modified script, please see it! I take CG simulations according to http://md.chem.rug.nl/marrink/coarsegrain.html. Thank you ! Then your structure should be built appropriately. -Justin 4

Re: [gmx-users] how to use atom2cg.awk

Justin A. Lemkul wrote: xi zhao wrote: But CG structure and native PDB structure is very different, please see my attaches. Remove the chain identifier from the input structure. You'll note that the x-coordinate of each atom in the output is the residue number, so the chain identifie

[gmx-users] Force groups?

Hi - I wonder if it is possible in Gromacs3/4 to write out the forces acting on a peptide due to its interaction with different components in the system e.g. waters, lipids, etc? If not, could someone comment on how difficult to would be to modify the source code to do this? Many thanks Chze Ling W

[gmx-users] Are Gromos 45a3 and GROMOS 53a6 compatible?

Hi GROMOS 45a3 force field GROMOS 53a6 force field Are they compatible? I notice that MOST of the force field parameters sets are THE SAME in the GROMOS 45a3 and GROMOS 53a6. So, I want to ask if GROMOS 53a6 is rectification from GROMOS 45a3. I mean if GROMOS 53a6 match more experimental data th

Re: [gmx-users] Are Gromos 45a3 and GROMOS 53a6 compatible?

Hi Lin, Well, actually G53a6 is heavily reparameterized... partly. So your observation that large portions of the force fields are equal is correct. That also makes the question of whether or not to mix them more difficult. It seems implicitly assumed by the authors that the parts of the force fie

RE: [gmx-users] Force groups?

Hi, Please do not send the same question to multiple mailing lists, (multiple) people might answer the same questions multiple times then. Here is my answer on gmx-developers: You will have to use mdrun -rerun with different tpr files where you on switch off all the interactions between all ener

Re: [gmx-users] grompp in gromacs-4.0.4

Thanks! The problem was indeed the spaces in the group names. Vaithee === S. Vaitheeswaran Post-doctoral Research Associate Center for Biotechnology and Interdisciplinary Studies Rensselaer Polytechnic Institute 110 8th Street, Troy NY 12180 Tel

Re: [gmx-users] Force groups?

Hi Berk - many thanks for your reply and apologies for cross-posting. Kind Regards Chze Ling On Mon, May 11, 2009 at 3:04 PM, Berk Hess wrote: > Hi, > > Please do not send the same question to multiple mailing lists, > (multiple) people might answer the same questions multiple times then. > Her

[gmx-users] where is the normalization direction in radial axial g_densmap plots?

I made a radial-axial density plot using g_densmap. What one gets out is a 3-D number density as a function of radial and axial distance from the defined axis. So which is the third direction, and how is it averaged out? Sorry if this is a very elementary question g_densmap -f protein.xtc -s prote

RE: [gmx-users] where is the normalization direction in radial axial g_densmap plots?

Hi, Well, there is axial, radial and angular (angle of rotation around the axial direction). Averaging happens over the radial coordinate. Berk Date: Mon, 11 May 2009 18:27:07 +0200 From: mariagorano...@gmail.com To: gmx-users@gromacs.org Subject: [gmx-users] where is the normalization directi

[gmx-users] restraining ligand for position restraint simulation

Hi, I think this was answered earlier but I didn't quite understand the answer given. Hi Hitesh, The posre.itp file only contains a header [ position_restraints ] followed by a list of atom numbers and restraint force constants. Check chapter 5 of the manual for how and what. For a ligand it's

[gmx-users] RDF in GMX 4

Hello, everyone, in earlier versions of the Gromacs the option to calculate rdf between center of mass (com-com) was not implemented. Is this option implemented in version 4.0? If no, someone would have suggestion to calculate the RDF com-com for liquid benzene? thanks EEF _

Re: [gmx-users] restraining ligand for position restraint simulation

Halie Shah wrote: I am trying to do what Hitesh tried to do..get a pos restraint on both my protein and ligandI found that -DPOSRES only takes into account 1 posre.itp file...so I appended the atom numbers of my ligand (2519-2531) to the end of the posre file for my protein (1-2518). The

Re: [gmx-users] RDF in GMX 4

Eudes Fileti wrote: Hello, everyone, in earlier versions of the Gromacs the option to calculate rdf between center of mass (com-com) was not implemented. Is this option implemented in version 4.0? If no, someone would have suggestion to calculate the RDF com-com for liquid benzene? From g_r

[gmx-users] How to create .pdb files?

I have tried to export .pdb files from ChemBio3D Ultra but it does not do a very good job. What is the best or simply a good, reliable method of generating a .pdb file? Thanks for your help :) Casey _ Insert movie times and more

Re: [gmx-users] How to create .pdb files?

Joseph Johnson wrote: I have tried to export .pdb files from ChemBio3D Ultra but it does not do a very good job. What is the best or simply a good, reliable method of generating a .pdb file? If it is simply a formatting issue, you can fix it yourself using the PDB format guidelines: http

Re: [gmx-users] How to create .pdb files?

Justin A. Lemkul wrote: Joseph Johnson wrote: I have tried to export .pdb files from ChemBio3D Ultra but it does not do a very good job. What is the best or simply a good, reliable method of generating a .pdb file? If it is simply a formatting issue, you can fix it yourself using the PD

Re: [gmx-users] Some molecules disconnected into many parts after EM

Dear Justin: - Program mdrun_d, VERSION 4.0.4 Source code file: gmx_fft_mkl.c, line: 825 Fatal error: Error executing Intel MKL FFT. --- I really could not find out what is the reason for the error above. Do you mean som

Re: [gmx-users] Some molecules disconnected into many parts after EM

Yanmei Song wrote: Dear Justin: - Program mdrun_d, VERSION 4.0.4 Source code file: gmx_fft_mkl.c, line: 825 Fatal error: Error executing Intel MKL FFT. --- I really could not find out what is the reason for the error

[gmx-users] RE: RE: RDF in GMX 4 (Justin)

Thanks for reply Justin. I had already read this part of the manual but I can´t understood it well. How can I take account the mentioned input file run? Would it be a kind of index file? Could you provide me an example? Bests eef ___ Eudes Eterno Fileti Centro de

[gmx-users] Protein-Ligand Docking?

HI When i visualize the MD trajectory, the protein and ligand are closed by. But, I don't know if ligand really DOCK on the protein. Please tell me how to define the successful docking. Thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org ht

[gmx-users] No default Angle types

Dear All, I ran grompp and was presented with the following error: ERROR 0 [file "graphene_nm_test.top", line 51217]: No default Angle types Line 51217 of the topology file is: 5116 5115 5117 1 and atoms 5115 to 5117 are defined in the topology file as: 5115 opls_145 1 Grph C 4859 -0.12 12.

RE: [gmx-users] RE: RE: RDF in GMX 4 (Justin)

Run input file = .tpr Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology and Pharmacology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only

Re: [gmx-users] Protein-Ligand Docking?

Chih-Ying Lin wrote: HI When i visualize the MD trajectory, the protein and ligand are closed by. But, I don't know if ligand really DOCK on the protein. "Docking" cannot be accomplished by Gromacs. If you wish to determine whether or not your ligand or protein are favorably associated, it

Re: [gmx-users] RE: RE: RDF in GMX 4 (Justin)

Eudes Fileti wrote: Thanks for reply Justin. I had already read this part of the manual but I can´t understood it well. How can I take account the mentioned input file run? Would it be a kind of index file? http://wiki.gromacs.org/index.php/.tpr_File http://wiki.gromacs.org/index.php/.ndx

Re: [gmx-users] No default Angle types

darre...@ece.ubc.ca wrote: Dear All, I ran grompp and was presented with the following error: ERROR 0 [file "graphene_nm_test.top", line 51217]: No default Angle types Line 51217 of the topology file is: 5116 5115 5117 1 and atoms 5115 to 5117 are defined in the topology file as: 5115 op

[gmx-users] TestBed in MPI not working

Hi everyone. Well, lets go straight to the point: last time I've installed gromacs, it was still 3.3.x and there was no testbed available yet. I've done some tests of my own and everything gone fine. I'm doing some new installations now, both gmx3.3.3 and gmx4.0.4. They weem to work pretty well i

Re: [gmx-users] TestBed in MPI not working

Jones de Andrade wrote: Hi everyone. Well, lets go straight to the point: last time I've installed gromacs, it was still 3.3.x and there was no testbed available yet. I've done some tests of my own and everything gone fine. I'm doing some new installations now, both gmx3.3.3 and gmx4.0.4.

RE: [gmx-users] Protein-Ligand Docking?

First step, define what you mean by being "DOCKed". Second step, determine if those conditions are meet by your protein and ligand. Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology and Pharmacology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Pa

Re: [gmx-users] TestBed in MPI not working

Thanks Justin. ;) Well, I'm using a simple script to run the tests. The script follows: ** #!/bin/tcsh source ../../tcshrc source /opt/chemistry/gmx404.ompi/bin/GMXRC.csh set path=( $path /opt/mpi/ompi131/bin ) setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/opt/mpi/ompi131/lib se

Re: [gmx-users] TestBed in MPI not working

Jones de Andrade wrote: Using just the "simple" tests now to try to find out where is the error. Since the error goes everywhere, it just simplify things. It outputs everything ok with the serial part, but it all gets really messy in the mpi section. In version 4.0.4, it's complaining tha

Re: [gmx-users] TestBed in MPI not working

Hi Justin This has been discussed several times on the list. The -np flag is no > longer necessary with grompp. You don't get an mdrun.out because the .tpr > file is likely never created, since grompp fails. Yes, I know that and that is what I would have expected. But what I'm running is the g

Re: [gmx-users] TestBed in MPI not working

Justin A. Lemkul wrote: Jones de Andrade wrote: Hi Justin This has been discussed several times on the list. The -np flag is no longer necessary with grompp. You don't get an mdrun.out because the .tpr file is likely never created, since grompp fails. Yes, I know that and th

Re: [gmx-users] TestBed in MPI not working

Hi Justin. Thanks a lot for that. It helped, but enough yet. :( Just made 4.0.4 tests reach the same "range of errors" that I'm getting with 3.3.3. :P Using openMPI, it just complains that it can't find orted. That would mean that the paths are not in there, BUT they are. :P If I just try to run

Re: [gmx-users] TestBed in MPI not working

Jones de Andrade wrote: Hi Justin. Thanks a lot for that. It helped, but enough yet. :( Just made 4.0.4 tests reach the same "range of errors" that I'm getting with 3.3.3. :P Using openMPI, it just complains that it can't find orted. That would mean that the paths are not in there, BUT they

Re: [gmx-users] TestBed in MPI not working

Hi Justin. Well, bothering again. Good and bad news. The good news: I found a strange "work-around" for my problems here. For some reason, the perl script updates the path, environments and everything else when runs. So, the variables I placed on the script I was using where simply lost. Workarou

Re: [gmx-users] how to use atom2cg.awk

I have discovered two other potential errors in the script: 1. Coordinates are not processed quite right; this leads to a molecule with the correct shape, but some residues are scrambled. 2. ILE residues are not handled correctly (only a backbone particle is generated) I modified the script,

Re: [gmx-users] TestBed in MPI not working

Ok, summary of errors begin here. First, errors with MPI in double precision: 1 Simple Test: bham: ns type Simple is not supported with domain decomposition, use particle decomposition: mdrun -pd 7 Complex Tests: acetonitrilRF: ns type Simple is not supported with domain decomposition, use parti

Re: [gmx-users] TestBed in MPI not working

Jones de Andrade wrote: Ok, summary of errors begin here. First, errors with MPI in double precision: 1 Simple Test: bham: ns type Simple is not supported with domain decomposition, use particle decomposition: mdrun -pd 7 Complex Tests: acetonitrilRF: ns type Simple is not supported with d

Re: [gmx-users] TestBed in MPI not working

Hi Justin. On Mon, May 11, 2009 at 11:10 PM, Justin A. Lemkul wrote: > All of the above can be fixed by changing the appropriate .mdp option. Yes, I agree. I'll try that. Probably that's what will solve that problem. If that's ok, I'll send to the site a "revised" version of the test set. :)

[gmx-users] protein falls apart in energy minimization

hi all I am running Gromacs on a protein consisted of three chains. But no matter how I tried, the protein always falls into three parts (corresponding to each chain) after a simple 2000 steps energy minimization. Can anyone help me please? Thanks. Zhong Zheng

[gmx-users] Re: Problem with protein in lipid bilayer simulation

Hello Justin, Thanks a lot for the reply. Your tutorial is indeed very good. I followed your tutorial on protein-lipid simulation. I added the non-bonded parameters from the lipid.itp file to the ffG53a6nb_lipid.itp file. You have told to either delete the atom-type HW entries having zero values i

[gmx-users] Coordinate covalent bond

Dear all, In pdb file. the metal ion form a coordinate covalent bond with SG of cystine. but seems pdb2gmx ignored CONNECT in pdb file. how to modify the .top or .itp to include the bond and parameterize the bond. I tried to find some tutorial for some special case like this. But I couldnot. C

Re: [gmx-users] TestBed in MPI not working

Jones de Andrade wrote: Hi Justin. Well, bothering again. Good and bad news. The good news: I found a strange "work-around" for my problems here. For some reason, the perl script updates the path, environments and everything else when runs. So, the variables I placed on the script I was usin

Re: [gmx-users] Coordinate covalent bond

Zhanglin Ni wrote: Dear all, In pdb file. the metal ion form a coordinate covalent bond with SG of cystine. but seems pdb2gmx ignored CONNECT in pdb file. how to modify the .top or .itp to include the bond and parameterize the bond. I tried to find some tutorial for some special case like this

Re: [gmx-users] protein falls apart in energy minimization

Zhong Zheng wrote: hi all I am running Gromacs on a protein consisted of three chains. But no matter how I tried, the protein always falls into three parts (corresponding to each chain) after a simple 2000 steps energy minimization. Can anyone help me please? Thanks. Are you seeing a visual

Re: [gmx-users] protein falls apart in energy minimization

hi, Defining a specific box size with -d option in editconf will help to overcome this problem... Regards, Pawan On Tue, May 12, 2009 at 8:05 AM, Zhong Zheng wrote: > hi all > > I am running Gromacs on a protein consisted of three chains. But no matter > how I tried, the protein always falls i

Re: [gmx-users] Re: Problem with protein in lipid bilayer simulation

Hi Anirban, I have also followed Justin sir's tutorial. You should not remove the OW entries. You can remove the HW entries for sure and then this will work. Regards, Pawan On Tue, May 12, 2009 at 9:45 AM, Anirban Ghosh wrote: > Hello Justin, > > Thanks a lot for the reply. Your tutorial is ind

Re: [gmx-users] No default Angle types

Hi Justin, Thanks for the quick reply. Yes, I was also thinking about using a different atom type such as the alkane types you mentioned below. However, when I thought about how I can include these atom types in my .n2t file, I recognized that this might cause a potential problem since now I woul

[gmx-users] lipid_posre.itp file

Dear all I need lipid_posre.itp file can anyone suggest me from where I can find it ?or If I have to make it by my own then please let me know how can I make it. If anyone can suggest me I really will be thankful for him. Nitu Sharma ___