Re: [gmx-users] pdb2gmx... cys-cys bonds....
sharada wrote: Hello gromacs users, I am trying to molecular dynamics simulations on a 30 residues protein. I am protonating all the six cysteins after breaking their disulphide bonds. This linear non-disulphide bond structure is my starting structure for my simulations. After a 5ns dynamics run I would like to take the final structure and subsequently form the native bonds again and simulate it further for 5 ns. Cys-Cys distances have increased considerably after the simulations. I am unable to form the cys-cys bonds using the pdb2gmx as the S-S distances are not within the disulphide bond range. There'd be a good reason for this... it would be an unphysically long bond, and the subsequent dynamics would be weird. If you want to re-form the bond, do some more MD with a short harmonic restraint between the two sulfur atoms, and then we they are close enough, alter the topology in the way you describe. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] pdb2gmx... cys-cys bonds....
Dear Dr. Mark Abraham, Thank you for the response. I am into desiging small antibacterial peptides with cysteins. I would have to play around with forming different combination of disulphide bonds and check the stereochemical properties and further design them experimentally to see if they are active. I have many peptides to build models of a lot of structures with different Cys-Cys combinations for my simulations as my starting structures. If I want to form only those cys-cys pairs then yes I would have done the MD with harmonic restraints and bring it near. I have to check the proximal cys-cys distances and then make a decision on building only those disulphide bonds whose S-S distance are in the range of 4A to 5A.Can I change the pdb2gmx program to make this decision? Is it possible to change the code? if so how do I incorporate these changes. I think the pdb2gmx program is checking for S-S distance to less than or equal to 2A and makes the bond . Am I right ? Is there a way out in this direction. Kindly help or any other suggestion is welcome. Anticipating for a reply. Regards, sharada Mark Abraham wrote: sharada wrote: Hello gromacs users, I am trying to molecular dynamics simulations on a 30 residues protein. I am protonating all the six cysteins after breaking their disulphide bonds. This linear non-disulphide bond structure is my starting structure for my simulations. After a 5ns dynamics run I would like to take the final structure and subsequently form the native bonds again and simulate it further for 5 ns. Cys-Cys distances have increased considerably after the simulations. I am unable to form the cys-cys bonds using the pdb2gmx as the S-S distances are not within the disulphide bond range. There'd be a good reason for this... it would be an unphysically long bond, and the subsequent dynamics would be weird. If you want to re-form the bond, do some more MD with a short harmonic restraint between the two sulfur atoms, and then we they are close enough, alter the topology in the way you describe. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] pdb2gmx... cys-cys bonds....
sharada wrote: Dear Dr. Mark Abraham, Thank you for the response. I am into desiging small antibacterial peptides with cysteins. I would have to play around with forming different combination of disulphide bonds and check the stereochemical properties and further design them experimentally to see if they are active. I have many peptides to build models of a lot of structures with different Cys-Cys combinations for my simulations as my starting structures. If I want to form only those cys-cys pairs then yes I would have done the MD with harmonic restraints and bring it near. I have to check the proximal cys-cys distances and then make a decision on building only those disulphide bonds whose S-S distance are in the range of 4A to 5A.Can I change the pdb2gmx program to make this decision? Is it possible to change the code? You don't really want to change pdb2gmx. You want to write a Perl script that automates the disulfide bond selection process, does the harmonic restraint MD, and then simulates using a vaguely sensible disulfide starting structure. if so how do I incorporate these changes. I think the pdb2gmx program is checking for S-S distance to less than or equal to 2A and makes the bond . Am I right ? You can edit specbond.dat yourself... the format isn't described in the manual, if I recall correctly, but it's pretty obvious... you just increase a 0.2 to 0.4 or some such. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: fudgeQQ (again ...)
Thanks, Janne! No, I tried not having [pairs] or having empty [pairs] because the manual says it's not necessary if generate pairs = yes. Lianqing On Thu, 7 Dec 2006, Janne Hirvi wrote: Hello! Just a simple question - Do you have [pairs]-section in your topology file? Janne Dear GMX-users, Here are a followup and more details for my problem. I really hope to get through this, so I can move on ... I report the electrostatic energy (Uq, kJ/mol) for a molecule using 3 codes. 1. Gromacs 3.3 [default] 1 1 yes 0.5 FudgeQQ FudgeQQ [moleculetype] Uq 0.0, 0.8333, or 1.0 mol 3116.050 0.0, 0.8333, or 1.0 mol 2 -413.048 2. DLPOLY with scaling factor of 0.8 Uq = -324.68 3. My own code Scaling factor Uq 0.0115.99 0.8-324.68 1.0-412.81 Apparently, Gromacs gives the value without 1-4 interactions with mol 3, and the value for full 1-4 interactions with mol 2, regardless of fudgeQQ. Did I not do something right when using Gromacs? Thanks A LOT for your help! BTW: the Gromacs website seems down. Lianqing On Wed, 29 Nov 2006, Lianqing Zheng wrote: Dear GMX-users, I'm doing normal mode analysis for one molecule and found the calculated electrostatic energy (at t=0) doesn't change at all regardless of the value for fudgeQQ. (I used 1 1 yes 0.5 0.8 for [default] and molecule 2 for [moleculetype].) If I use molecule 3, the value will change but is still independent of fudgeQQ. Any idea what the problem is? I'll be happy to send you the input files if you need them. Thanks a lot! Lianqing ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] GROMACS with MPI/GAMMA
I recently ran GROMACS benchmarks (villin and DPPC) using Gigabit Ethernet with TCP and GAMMA protocols. GAMMA gives significantly better scaling than TCP as can be seen from the following sample timings. The serial results are in the usual nanosecs/day units and the speedup is measured with respect to the serial time. The nodes were dual-core P4D (3.0GHz) with Intel Pro 1000 NICS. The switch was Extreme Networks x450a-48t. I also compared with dual Opterons (2 X 275) with 4 cores per node and an Infiniband interconnect. Multi-node runs use all the cores on an individual node. Serial: Intel P4DOpteron 275 DPPC 0.2090.257 Villin10.1011.49 Speedup DPPC: Intel P4D Opteron 275 CPUS LAM OpenMPI MPI/GAMMA Infiniband 2 2.33 2.352.33 2.33 44.27 4.314.34 4.39 6 5.74 87.52 7.527.858.23 129.50 7.88 10.5 9.42 16 11.27.67 12.910.4 20 7.85 14.3 24 8.179.24 15.412.7 32 4.44 11.016.213.4 40 9.17 15.0 48 6.70 13.213.8 64 4.17 10.011.5 Speedup Villin: Intel P4D Opteron 275 CPUS LAM OpenMPI MPI/GAMMA Infiniband 2 1.94 1.872.05 1.95 42.52 2.332.73 3.27 6 2.85 82.85 2.473.464.24 122.52 2.153.334.00 161.94 1.792.744.00 20 1.402.20 240.32 1.081.733.00 32 0.661.112.00 --- Tony Ladd Chemical Engineering University of Florida PO Box 116005 Gainesville, FL 32611-6005 Tel: 352-392-6509 FAX: 352-392-9513 Email: [EMAIL PROTECTED] Web: http://ladd.che.ufl.edu ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] How to construct PMF from the result of AFM pulling?
Dear all: I have some problems about how to construct PMF(Potential of Mean Force) from the result of AFM pulling function in Gromacs.After the pull.pdo file was obtained and the force was calculated using the scripts writen by Prof. , How can I get the PMF from the result(coordinate and force)? In theory, Should I have to perform several AFM pulling simulation from different start points(conformation and velocity)?? Thanks!I will appreciate it if some one would help me solve this problem? ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] GROMACS with MPI/GAMMA
I sent the previous message before including comments: The Opteron 275 is 10-25% faster than the P4D for GROMACS. However the Opteron loses some of its edge when running dual threads. MPI/GAMMA outperforms both LAM and OpenMPI by a significant margin on DPPC and Villin benchmarks. With DPPC MPI/GAMMA scales as well as Infiniband but for Villin it is about 75% of the Infiniband performance. The reduced latency and more efficient flow control with the GAMMA protocol makes a significant difference to the scalability of Gigabit ethernet. In general the Intel NICS with GAMMA perform better than proprietary RDMA NICS from Ammasso and Level 5 networks. I had to make a small change to Gromacs 3.3 to get MPI/GAMMA to run. In futil.c line 102 the code tries to close a NULL pointer which strictly speaking is illegal. This causes GAMMA to hang. It seems harmless to comment it out. More details can be found at http://ladd.che.ufl.edu/research/beoclus/beoclus.htm The GAMMA website is http://www.disi.unige.it/project/gamma/mpigamma Tony --- Tony Ladd Chemical Engineering University of Florida PO Box 116005 Gainesville, FL 32611-6005 Tel: 352-392-6509 FAX: 352-392-9513 Email: [EMAIL PROTECTED] Web: http://ladd.che.ufl.edu ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: fudgeQQ (again ...)
Hi! I am not exactly sure but I think that there should be [pairs] section with all pairs named and the function number (=1) included but without any parameters which are then generated by Gromacs if generate pairs = yes. You can check from the .log -file if you have any 1-4 Coulombic (or 1-4 Lennard-Jones) interactions included in your case. Janne Thanks, Janne! No, I tried not having [pairs] or having empty [pairs] because the manual says it's not necessary if generate pairs = yes. Lianqing On Thu, 7 Dec 2006, Janne Hirvi wrote: Hello! Just a simple question - Do you have [pairs]-section in your topology file? Janne Dear GMX-users, Here are a followup and more details for my problem. I really hope to get through this, so I can move on ... I report the electrostatic energy (Uq, kJ/mol) for a molecule using 3 codes. 1. Gromacs 3.3 [default] 1 1 yes 0.5 FudgeQQ FudgeQQ [moleculetype] Uq 0.0, 0.8333, or 1.0 mol 3116.050 0.0, 0.8333, or 1.0 mol 2 -413.048 2. DLPOLY with scaling factor of 0.8 Uq = -324.68 3. My own code Scaling factor Uq 0.0115.99 0.8-324.68 1.0-412.81 Apparently, Gromacs gives the value without 1-4 interactions with mol 3, and the value for full 1-4 interactions with mol 2, regardless of fudgeQQ. Did I not do something right when using Gromacs? Thanks A LOT for your help! BTW: the Gromacs website seems down. Lianqing On Wed, 29 Nov 2006, Lianqing Zheng wrote: Dear GMX-users, I'm doing normal mode analysis for one molecule and found the calculated electrostatic energy (at t=0) doesn't change at all regardless of the value for fudgeQQ. (I used 1 1 yes 0.5 0.8 for [default] and molecule 2 for [moleculetype].) If I use molecule 3, the value will change but is still independent of fudgeQQ. Any idea what the problem is? I'll be happy to send you the input files if you need them. Thanks a lot! Lianqing ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] GROMACS exit codes; error in LAM installation?
Hello, (background) I recently compiled a new version of the 3.2.1 mdrun to make use of the lam 7.1.2 that's just been installed. For some reason, I can't get a run to work with it - it goes fine until: Back Off! I just backed up enerG.edr to ./#enerG.edr.1# starting mdrun '?' 143 steps, 2145.0 ps. whereupon one of the processes (always n3, no matter which physical machine it is) exits for no obvious reason. The signal given is 11 - I can't find reference to this in the Gromacs or lam source, so I don't know what it means. Cranking up the verbosity on everything I can sheds no further light on it. I'm guessing I did something not quite right in the installation, but without more information, there's no way to know how to fix it. Anyway: So, does anyone know what this exit code means? (and, ideally, how to avoid it...) Do you Yahoo!? Everyone is raving about the all-new Yahoo! Mail beta. http://new.mail.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] How to simulate a protein that contains two cuban cluster
Hei, I want to simulate a protein that contains two cuban clusters with gromacs, so I want to know which forcefield is recommended to use for Fe-S compounds. On the other hand I can use Gaussian software using the UFF forcefield. Because i am new to this field (master student doing an internship) I would like to know which is better to use, it's only to treat the whole protein plus clusters mechanically. Later I will use Oniom methods with gaussian. Hope someone has the answer... :) Stefan -- Ein Herz für Kinder - Ihre Spende hilft! Aktion: www.deutschlandsegelt.de Unser Dankeschön: Ihr Name auf dem Segel der 1. deutschen America's Cup-Yacht! ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: fudgeQQ (again ...)
Thanks a lot, Janne! I finally got it! Thanks for your inspiration! I added 1-4 pairs in [pairs] and then got the right values. I thought Gromacs would automatically find 1-4 pairs. Lianqing On Thu, 7 Dec 2006, Janne Hirvi wrote: Hi! I am not exactly sure but I think that there should be [pairs] section with all pairs named and the function number (=1) included but without any parameters which are then generated by Gromacs if generate pairs = yes. You can check from the .log -file if you have any 1-4 Coulombic (or 1-4 Lennard-Jones) interactions included in your case. Janne Thanks, Janne! No, I tried not having [pairs] or having empty [pairs] because the manual says it's not necessary if generate pairs = yes. Lianqing On Thu, 7 Dec 2006, Janne Hirvi wrote: Hello! Just a simple question - Do you have [pairs]-section in your topology file? Janne Dear GMX-users, Here are a followup and more details for my problem. I really hope to get through this, so I can move on ... I report the electrostatic energy (Uq, kJ/mol) for a molecule using 3 codes. 1. Gromacs 3.3 [default] 1 1 yes 0.5 FudgeQQ FudgeQQ [moleculetype] Uq 0.0, 0.8333, or 1.0 mol 3116.050 0.0, 0.8333, or 1.0 mol 2 -413.048 2. DLPOLY with scaling factor of 0.8 Uq = -324.68 3. My own code Scaling factor Uq 0.0115.99 0.8-324.68 1.0-412.81 Apparently, Gromacs gives the value without 1-4 interactions with mol 3, and the value for full 1-4 interactions with mol 2, regardless of fudgeQQ. Did I not do something right when using Gromacs? Thanks A LOT for your help! BTW: the Gromacs website seems down. Lianqing On Wed, 29 Nov 2006, Lianqing Zheng wrote: Dear GMX-users, I'm doing normal mode analysis for one molecule and found the calculated electrostatic energy (at t=0) doesn't change at all regardless of the value for fudgeQQ. (I used 1 1 yes 0.5 0.8 for [default] and molecule 2 for [moleculetype].) If I use molecule 3, the value will change but is still independent of fudgeQQ. Any idea what the problem is? I'll be happy to send you the input files if you need them. Thanks a lot! Lianqing ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] charges for non-natural residues with gromos 53a6
dear all//
i need to parameterize a non-natural amino acid residue.
i have a problem with assigning the charges, how should i scale them? i
can obtain quantum chemical charges from AM1 to {HF,DFT}/6-31G* and
further, but how to include (scaling, i now where to write them) them in
the force field?
thanks a lot//
carsten
--
dr carsten baldauf
biotechnologisches zentrum der tu dresden
http://www.biotec.tu-dresden.de/pisabarro
http://www.biotec.tu-dresden.de/~carstenb
Please avoid sending me Word or PowerPoint attachments.
See http://www.gnu.org/philosophy/no-word-attachments.html
No Software Patents!
See http://www.ffii.org/index.en.html
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] GROMACS exit codes; error in LAM installation?
On Thu, Dec 07, 2006 at 08:30:30AM -0800, Alan Dodd wrote: whereupon one of the processes (always n3, no matter which physical machine it is) exits for no obvious reason. The signal given is 11 - I can't find reference to this in the Gromacs or lam source, so I don't know what it means. Cranking up the verbosity on everything I can sheds no further light on it. I'm guessing I did something not quite right in the installation, but without more information, there's no way to know how to fix it. Signal 11 is a segfault, i.e. something goes very wrong. It's hard to say anything definite at this point, but are you sure that the mpicc and lamboot you use belong to the same version of lam? If there is an old lamd (say, 7.1.1) hanging around, using a 7.1.2 mpicc might lead to a crash. A. -- Ansgar Esztermann Researcher Sysadmin http://www.mpibpc.mpg.de/groups/grubmueller/start/people/aeszter/index.shtml pgpCxWdLeGCSe.pgp Description: PGP signature ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] charges for non-natural residues with gromos 53a6
the problems gets more difficult to me ... :-(
i want to substitute a single peptide bond in a normal sequence with an
ester bond. i have problems finding the right parameters for an ester
bond, does somebody has done something similar? i would be very happy
about any help.
thanks in advance//
carsten
dear all//
i need to parameterize a non-natural amino acid residue.
i have a problem with assigning the charges, how should i scale them? i
can obtain quantum chemical charges from AM1 to {HF,DFT}/6-31G* and
further, but how to include (scaling, i now where to write them) them in
the force field?
thanks a lot//
carsten
--
dr carsten baldauf
biotechnologisches zentrum der tu dresden
http://www.biotec.tu-dresden.de/pisabarro
http://www.biotec.tu-dresden.de/~carstenb
Please avoid sending me Word or PowerPoint attachments.
See http://www.gnu.org/philosophy/no-word-attachments.html
No Software Patents!
See http://www.ffii.org/index.en.html
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: fudgeQQ (again ...)
Thanks a lot, Janne! I finally got it! Thanks for your inspiration! I added 1-4 pairs in [pairs] and then got the right values. I thought Gromacs would automatically find 1-4 pairs. send the structure to pdb2gmx and the value of genpairs will be determined from your ffXXX.itp file. As far as I know, this is only in this way that the [pairs] section will be generated in the output.top file. If your system is not a protein, then you need to add the paris section (and in fact create the entire .top file) by hand. By the way, why are you using the combination of genpairs=yes fudgeLJ=0.5 and fudgeQQ=0.8333 ? This is not a valid combination for any force field that comes in the standard gromacs distribution. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: fudgeQQ (again ...)
2006/12/7, [EMAIL PROTECTED] [EMAIL PROTECTED]: By the way, why are you using the combination of genpairs=yes fudgeLJ=0.5 and fudgeQQ=0.8333 ? This is not a valid combination for any force field that comes in the standard gromacs distribution. Hi, I am puzzled about this. In your opinion, when I use genpairs=no, fudgeLJ= 0.5 and fudgeQQ=0.8333, are these scaling factors, 0.5 and 0.8333, useful? On the other hand, when using genpairs=yes, how to set the scaling factor of fudgeLJ and fudgeQQ?$ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: fudgeQQ (again ...)
Thanks, Chris! I'm using AMBER FF, so those are the scaling factors in this force field. Actually I never used standard Gromacs/Gromos ff and always make my own top file from scratch. Lianqing On Thu, 7 Dec 2006 [EMAIL PROTECTED] wrote: Thanks a lot, Janne! I finally got it! Thanks for your inspiration! I added 1-4 pairs in [pairs] and then got the right values. I thought Gromacs would automatically find 1-4 pairs. send the structure to pdb2gmx and the value of genpairs will be determined from your ffXXX.itp file. As far as I know, this is only in this way that the [pairs] section will be generated in the output.top file. If your system is not a protein, then you need to add the paris section (and in fact create the entire .top file) by hand. By the way, why are you using the combination of genpairs=yes fudgeLJ=0.5 and fudgeQQ=0.8333 ? This is not a valid combination for any force field that comes in the standard gromacs distribution. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: fudgeQQ (again ...)
I am puzzled about this. In your opinion, when I use genpairs=no, fudgeLJ= 0.5 and fudgeQQ=0.8333, are these scaling factors, 0.5 and 0.8333, useful? On the other hand, when using genpairs=yes, how to set the scaling factor of fudgeLJ and fudgeQQ?$ fudgeQQ is always used no matter what the value of genparis is. (exerpt from http://www.gromacs.org/pipermail/gmx-users/2006-September/023743.html) Each force-field has its own rules (e.g. gen-pairs and FudgeLJ/QQ), but these apply to the information outlined above. For example, gen-pairs does NOT mean generate a [ pairs ] section for the molecule. Instead, it means If LJ-14 epsilon and sigma are not present in a [ pairs ] section entry, and that type of interaction is not explicitly formulated in [ pairtypes ], then it is permissible to use the regular non-bonded parameters, and in that case scale them by FudgeLJ. Therefore your settings indicate that coulombic 1-4 interactions will be scaled by 0.8333 and the pairs must be taken directly from the [ pairs ] or [ pairtypes ] section (and they will NOT be scaled by fudgeLJ). In your case fudgeLJ does not matter (you could change the value and it would not affect your simulation). However, I have always hoped that it is set to 0.5 to indicate that this is what the forcefield developers have done for you and included it in [ pairtypes ] so that it's kind of a reference value for your piece of mind. I was assuming that the previous messages were from an Amber forcefield. Since Amber uses (to my knowledge) [ pairtypes ] instead of genpairs=yes, I was confused by the combination of genpairs=yes and fudgeQQ=0.8333. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] How to simulate a protein that contains two cuban cluster
Stefan Schöbel wrote: Hei, I want to simulate a protein that contains two cuban clusters with gromacs, so I want to know which forcefield is recommended to use for Fe-S compounds. Probably, none of them. One has to develop parameters for these atom types based on experimental or high-level computational data. The odds against data on compounds even vaguely resembling yours a) existing, and b) being included in any current force field, are geological. Accordingly, the odds against any current parameters providing an adequate physical model are cosmological. On the other hand I can use Gaussian software using the UFF forcefield. Because i am new to this field (master student doing an internship) I would like to know which is better to use, it's only to treat the whole protein plus clusters mechanically. Whoever set this task appears either to know little about the utility of MM forcefields, or to want to teach you about said utility :-) Later I will use Oniom methods with gaussian. This is where you should start. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] GROMACS exit codes; error in LAM installation?
Alan Dodd wrote: Hello, (background) I recently compiled a new version of the 3.2.1 mdrun to make use of the lam 7.1.2 that's just been installed. For some reason, I can't get a run to work with it - it goes fine until: Back Off! I just backed up enerG.edr to ./#enerG.edr.1# starting mdrun '?' 143 steps, 2145.0 ps. whereupon one of the processes (always n3, no matter which physical machine it is) exits for no obvious reason. The signal given is 11 - I can't find reference to this in the Gromacs or lam source, so I don't know what it means. Cranking up the verbosity on everything I can sheds no further light on it. I'm guessing I did something not quite right in the installation, but without more information, there's no way to know how to fix it. Anyway: So, does anyone know what this exit code means? (and, ideally, how to avoid it...) I'd do a re-install of MPI, FFTW and GROMACS, and upgrade to GROMACS version 3.3.1 while I was at it :-) Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] error in pdb2gmx
Please, give an adive. I've add new residues to ffoplsaa.rtp build pdb file. and try to convert it to gromacs format. under WindowsXP, using GROMACS 3.2.1 everyting is OK. but, when i did the same comman under GROMACS 3.3.1 (SuSE), i've got an error: Read 4904 atoms Opening library file /usr/local/gromacs/share/gromacs/top/xlateat.dat 26 out of 26 lines of xlateat.dat converted succesfully Analyzing pdb file There are 1 chains and 0 blocks of water and 258 residues with 4904 atoms chain #res #atoms 1 ' ' 258 4904 All occupancy fields zero. This is probably not an X-Ray structure Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaa.atp Atomtype 817 Reading residue database... (ffoplsaa) Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaa.rtp --- Program pdb2gmx, VERSION 3.3.1 Source code file: resall.c, line: 289 Fatal error: in .rtp file at line: --- These Gromacs Guys Really Rock (P.J. Meulenhoff) What I'm doing wrong? -- Dmitriy Golubovsky ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] error in pdb2gmx
Dmitriy Golubobsky wrote: Please, give an adive. I've add new residues to ffoplsaa.rtp build pdb file. and try to convert it to gromacs format. under WindowsXP, using GROMACS 3.2.1 everyting is OK. but, when i did the same comman under GROMACS 3.3.1 (SuSE), i've got an error: Read 4904 atoms Opening library file /usr/local/gromacs/share/gromacs/top/xlateat.dat 26 out of 26 lines of xlateat.dat converted succesfully Analyzing pdb file There are 1 chains and 0 blocks of water and 258 residues with 4904 atoms chain #res #atoms 1 ' ' 258 4904 All occupancy fields zero. This is probably not an X-Ray structure Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaa.atp Atomtype 817 Reading residue database... (ffoplsaa) Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaa.rtp --- Program pdb2gmx, VERSION 3.3.1 Source code file: resall.c, line: 289 Fatal error: in .rtp file at line: --- These Gromacs Guys Really Rock (P.J. Meulenhoff) What I'm doing wrong? This is only a guess, but if your .rtp file uses Windows line-endings and pdb2gmx is sensitive to that, you might see such a problem. Use dos2unix on all your ex-Windows files and see how you go. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Can I use different force field functions for a molecule
Dear I want to know whether I can use different functions in a molecule without making extra code.For example in a methanol molecule,I want to use Harmonic potential for C-H bond and use Morse pontential for C-OH bond. Besides,in user specified potential functions,I want to know whether I can use different potential functions without extra code.Thank you. Kind Regards ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Can I use different force field functions for a molecule
intelandamd wrote: Dear I want to know whether I can use different functions in a molecule without making extra code.For example in a methanol molecule,I want to use Harmonic potential for C-H bond and use Morse pontential for C-OH bond. Besides,in user specified potential functions,I want to know whether I can use different potential functions without extra code.Thank you. Yes. Read chapter 5 of the manual. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Simulation of two peptides
Dear all When we simulate two or more peptides/structures together, does gromacs select the best possible orientations of the structures. Regards nur - Find out what India is talking about on - Yahoo! Answers India Send FREE SMS to your friend's mobile from Yahoo! Messenger Version 8. Get it NOW___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
