Re: [gmx-users] GROMACS file formats

Mark Abraham wrote: Santanu Ch wrote: Hi, I am looking for the documentation of GROMACS trajectory output file format and GROMACS .tpr file format. We have our own MD simualation program which is based on CHARMM. We would like to make this program output simulation trajectories in

Re: [gmx-users] simulation of protein in presence of ATP

nikhil damle wrote: Hi, We can use max 4 coloumns for naming atoms. But .rtp file has 5 coloumn atom names (AO1PG etc) That i modified to 4 letter name. But now the error is atom N not found in residue 1ATP while combining tdb and rtp pdb2gmx tries to cap termini of peptides

[gmx-users] Parameters for -Si-Si- chains?

Dear All, Our colleges asked me to do some rather simple MD of the organic-silicone compounds (-Si-Si-Si- backbone with organic radicals), but it appeared to be not so simple because of the force field. Does anybody know about parameters for such systems, which are adapted for GROMACS? I've

Re: [gmx-users] Parameters for -Si-Si- chains?

Hi Semen, When confronted with Si-Si-Si and radicals in the same sentence, I don't get comforted and definitely wouldn't characterize it as 'rather simmple' ;) There seem to be quite a number of publications referring to MD of Si-Si systems though. Try googling a bit, or try Web of Science; gives

RE: [gmx-users] How to increase the number of parameters in dihedral angle potentials?

Hi, I already answered this mail, but somehow for a small fraction of the mails I reply to hotmail replies to the user, not to the list. Here is my answer: You can't do this easily. The current maximum for the number of parameters per interaction is 6. If you really want to, you could increase

[gmx-users] How to freeze the atoms?

nbsp;Dear all nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; I attach 8 carbonyl groups onto a carbon nanotube (CNT). Each carbonyl group is considered as a residue named Car and each carbon atomnbsp;in the CNT is considered as a residue named Gr1. In the mdp file, the freezegrps are Gr1 and Car, and the

Re: [gmx-users] How to freeze the atoms?

toby10222...@sina.com wrote: Dear all I attach 8 carbonyl groups onto a carbon nanotube (CNT). Each carbonyl group is considered as a residue named Car and each carbon atom in the CNT is considered as a residue named Gr1. In the mdp file, the freezegrps are Gr1 and Car, and the

[gmx-users] Problem in energy minimization for a empty membrane system

Hi! I'm a postgraduate student from Malaysia and currently facing energy minimization problem for my membrane system. I'm trying to perform energy minimization for an empty POPC membrane with position restraint on the lipid. Minimization stop due to inf Fmax. And I noticed that in the log file as

Re: [gmx-users] simulation of protein in presence of ATP

Thanks a lot for kind help. I reached till grompp before minimizing energy of the system where I received an error msg as Invalid order for directive defaults: filename; line x !!! what is the meaning of this error ? Is it something to do with path variable problem or

[gmx-users] Re: How to freeze the atoms?

Dear all nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; I attach 8 carbonyl groups onto a carbon nanotube (CNT). Each carbonyl group is considered as a residue named Car and each carbon atomnbsp;in the CNT is considered as a residue named Gr1. In the mdp file, the freezegrps are Gr1 and Car, and the

Re: [gmx-users] simulation of protein in presence of ATP

nikhil damle wrote: Thanks a lot for kind help. I reached till grompp before minimizing energy of the system where I received an error msg as Invalid order for directive defaults: filename; line x !!! what is the meaning of this error ? Is it something to do with path

Re: [gmx-users] Problem in energy minimization for a empty membrane system

Bing Bing wrote: Hi! I'm a postgraduate student from Malaysia and currently facing energy minimization problem for my membrane system. I'm trying to perform energy minimization for an empty POPC membrane with position restraint on the lipid. Minimization stop due to inf Fmax. And I noticed

RE: [gmx-users] pullx.xvg Meaning of output?

Hi, This is actually not (yet) documented. 0Z is the Z-coordinate of group 0. 1dZ is the the Z-coordinate of group 1 minus the one of group 0. Berk Date: Tue, 23 Jun 2009 12:54:37 +0200 From: ilona.bal...@bioquant.uni-heidelberg.de To: gmx-users@gromacs.org Subject: [gmx-users] pullx.xvg

RE: [gmx-users] pullx.xvg Meaning of output?

Dear Berk, Thanks for the quick reply. That leads me to my next questions: *I used the whole N and C residues for pulling. Is there any way of reconstructing the values for the single atoms? Or do you recommend only to pull N and C in the first place? *What does the reference group actually

[gmx-users] genbox error at futil.c

Hi! I am a very beginner, trying to make some dynamics of a protein in a water box, after doing some (web) tutorials. I googled first for this (possibly simple) error, found one reference, but cannot see it, possibly because the gromacs site is under changes. I ran pdb2gmx and editconf.

Re: [gmx-users] Parameters for -Si-Si- chains?

ThanksTsjerk, Google is definitely our best friend :) However, digging for parameters and testing the funny mixed force field is not justified in this case - the project is small as well as the amount of financing :) So, I whould be very grateful if somebody could point me to the ready-to-use

Re: [gmx-users] genbox error at futil.c

iulek wrote: Hi! I am a very beginner, trying to make some dynamics of a protein in a water box, after doing some (web) tutorials. I googled first for this (possibly simple) error, found one reference, but cannot see it, possibly because the gromacs site is under changes. I ran

Re: [gmx-users] Problem in energy minimization for a empty membrane system

Hi Justin, I've tried with no restraint and the minimization stopped at the same time. I actually suspect that the restraint is not working at all. My top file is as below:- #include ffG53a6_lipid.itp #include popc.itp #ifdef POSRES #include posres_popc.itp #endif #ifdef FLEX_SPC #include

[gmx-users] parallel processing using LAN

For parallel processing is it possible to use the system connected to the local area network something like clustering the system for simulation. plz suggest me so that i can use my resources for faster simulation. thanks AKALABYA BISSOYI N.I.T.Rourkela.

Re: Re: [gmx-users] genbox error at futil.c

Thanks for replying. Humm..., maybe I see now. As a beginner I intended to keep all files produced and better inspect what happens in sequence, but I did not want to use the conventional renaming. But it seems that for the topology file, the common procedure is to keep always one only

Re: [gmx-users] Parameters for -Si-Si- chains?

* Semen Esilevsky yesi...@yahoo.com [2009-06-23 06:06:58 -0700]: ThanksTsjerk, Google is definitely our best friend :) However, digging for parameters and testing the funny mixed force field is not justified in this case - the project is small as well as the amount of financing :) So, I

Re: [gmx-users] Problem in energy minimization for a empty membrane system

Bing Bing wrote: Hi Justin, I've tried with no restraint and the minimization stopped at the same time. I actually suspect that the restraint is not working at all. My top file is as below:- #include ffG53a6_lipid.itp #include popc.itp #ifdef POSRES #include posres_popc.itp #endif #ifdef

Re: [gmx-users] genbox error at futil.c

iulek wrote: Thanks for replying. Humm..., maybe I see now. As a beginner I intended to keep all files produced and better inspect what happens in sequence, but I did not want to use the conventional renaming. But it seems that for the topology file, the common procedure is to keep

Re: [gmx-users] Problem in energy minimization for a empty membrane system

Thanks for reply. I've used editconf to define the box by issuing :- editconf -f popc.pdb -o popc_box.gro -c -d 1.0 -bt cubic Is this the correct way of using editconf? And with this i proceed with grompp with the mdp file from previous email followed by mdrun Actually the restraint is

Re: [gmx-users] simulation of protein in presence of ATP

OK till here done ! the pdb file generated for EM should have ATP molecule @proper position as input .top file has the ATP.itp included. It did not have. If I do -ci it would randomly replace the solvent. I want ATP @ its proper location. how do i do this ?

RE: [gmx-users] pullx.xvg Meaning of output?

Hi, Everything depends on what you want to accomplish, which you do not write. I don't see why you would want to look at single atoms. Since you pull on COM's, only the COM coordinates are relevant. If you want to look at single atoms, simply store them in the xtc file. If you have only two

Re: [gmx-users] Problem in energy minimization for a empty membrane system

Bing Bing wrote: Thanks for reply. I've used editconf to define the box by issuing :- editconf -f popc.pdb -o popc_box.gro -c -d 1.0 -bt cubic Is this the correct way of using editconf? This would be appropriate for a protein, but not a membrane. What you're doing is defining a layer of

Re: [gmx-users] simulation of protein in presence of ATP

nikhil damle wrote: OK till here done ! the pdb file generated for EM should have ATP molecule @proper position as input .top file has the ATP.itp included. It did not have. If I do -ci it would randomly replace the solvent. I want ATP @ its proper location. how do i do this ?

Re: [gmx-users] simulation of protein in presence of ATP

nikhil damle wrote: OK till here done ! the pdb file generated for EM should have ATP molecule @proper position as input .top file has the ATP.itp included. It did not have. If I do -ci it would randomly replace the solvent. I want ATP @ its proper location. how do i do this ? Like I implied

Re: [gmx-users] parallel processing using LAN

akalabya bissoyi wrote: For parallel processing is it possible to use the system connected to the local area network something like clustering the system for simulation. plz suggest me so that i can use my resources for faster simulation. Yes it's possible, but you will not scale to more than

[gmx-users] impose a external magnetic field

Dear all, I want to impose a homogeneous static magnetic field on a solution. I just wonder if the gromacs can do it, anyway? I believe gromacs can. However, could anyone give me some suggestions to do it? Thanks a lot! ___

Re: [gmx-users] impose a external magnetic field

风 大 wrote: Dear all, I want to impose a homogeneous static magnetic field on a solution. I just wonder if the gromacs can do it, anyway? I believe gromacs can. However, could anyone give me some suggestions to do it? This is not implemented. I assume you would want to add a Lorentz force?

[gmx-users] mdrun -c option did not work

Hello everyone, this is my very first post on GROMACS mailing list, so please apologize if my question seems very simple. Here is my problem... I ran a calculation using GROMACS 4.0.3 and this command line: mpirun -np 32 mdrun -s prot_md.tpr -c prot_md.gro -g md.log -e md.edr -o prot_md.trr

Re: [gmx-users] mdrun -c option did not work

Jérôme Baffreau wrote: Hello everyone, this is my very first post on GROMACS mailing list, so please apologize if my question seems very simple. Here is my problem... I ran a calculation using GROMACS 4.0.3 and this command line: mpirun -np 32 mdrun -s prot_md.tpr -c prot_md.gro -g

[gmx-users] WARNING: negative index -1 in group System

Hi, Allow me to be the first to archive a message with negative index. I ask for an index file: make_ndx_s -f ???.pdb -o ???.ndx and specify: a AG to select all the silver atoms into a group. The index file then clearly numbers and lists the atoms: all in [ system ], again all atom numbers in

[gmx-users] Re: WARNING: negative index -1 in group System

Sorry to post again, But I meant to say that for atom indexing I looked using gmxdump: gmxdump_s -s ???.tpr -f ???.pdb -nr and found only indexing starting at zero; e.g atom[0]={name=AG} Cheers, Chris Rowan University of Victoria 2009/6/23 Christopher Rowan chriskro...@gmail.com: Hi,

Re: [gmx-users] WARNING: negative index -1 in group System

Christopher Rowan wrote: Hi, Allow me to be the first to archive a message with negative index. I ask for an index file: make_ndx_s -f ???.pdb -o ???.ndx and specify: a AG to select all the silver atoms into a group. The index file then clearly numbers and lists the atoms: all in [ system ],

Re: 回复：[gmx-users] Re: How to freeze the atoms ?

I do not know such effect although work with the 'freeze' option for a number of years in many gromacs versions. Are you sure that the numbers of the atoms in your ndx file are the same as in the corresponding residues? I suggest that you should look for a problem there. Do the atoms move only

Re: [gmx-users] Problem in energy minimization for a empty membrane system

Hi! Thanks for your suggestion on the tutorial. I will try it out. I actually tried to use the starting structure without going through editconf and alteration but it failed. Here's the error: ERROR: The cut-off length is longer than half the shortest box vector or longer than the smallest box