[gmx-users] connecting two chains
Dear gmx users I am performing a simulation protein- ligand by gromacs. this protein contain two chains (A B) which separated from eachother. I did the following steps for pdb file 1- pdb2gmx –ignh –f initial.pdb –o initial.pdb –p topol.top -ter 2- editconf -bt cubic –f initial.pdb –o initial.pdb -c –d 0.9 3- genbox –cp initial.pdb –cs spc216.gro –o initial-box.pdb –p topol.top 4- grompp –f em.mdp –c initialbox.pdb –p topol.top –o xion.tpr 5- genion -s xion.tpr -o initial_ions.gro -p topol.top -pname NA -nname CL -nn (number of charge) everything was perfect, but the final pdb file has a problem which two chains are connected eachother. I would like to know how to solve these problems? regards -- Somayeh Alimohammadi Ph.D Student of Medical Nanotechnology Shahid Beheshti University of Medical Sciences Tehran-Iran -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Re : NPT Simulation average pressure lower than Reference set pressure
On 11/1/14 11:56 PM, Agnivo Gosai wrote: Dear Users I am sharing a few plots through Google Drive. If you are able to view the files then kindly comment. My workflow is as follows :- 1) Topolgy preparation with AMBER99SB-Parmbsc0 ff in GROMACS 4.5.6. TIP3P water model. 2) Putting the complex in a box , using spc216 to solvate , adding ions. 3) Energy minimization with steepest descent. 4) 100 ps NVT equilibration with V-rescale thermostat. Ref T = 300 K , Avg. T = 299.7 K and Total Energy also remained constant. 5) 1st NPT simulation with Berendsen barostat (Ref. Pressure = 1 bar) having the following results : ( A)Statistics over 50001 steps [ 0. through 100. ps ], 1 data sets All statistics are over 10001 points Energy Average Err.Est. RMSD Tot-Drift -- Pressure-5.57066.284.808538.1219 (bar) (B)All statistics are over 10001 points Energy Average Err.Est. RMSD Tot-Drift -- Density 1012.13 0.551.871723.17412 (kg/m^3) 6) 2nd NPT simulation with Parrinello-Rahman barostat (Ref. Pressure = 1 bar) having the following results : These are the average values :- Energy Average Err.Est. RMSD Tot-Drift -- Pressure -0.299523 0.64 93.313 -1.18081 (bar) Energy Average Err.Est. RMSD Tot-Drift --- Density 1012.32 0.261.685760.82485 (kg/m^3) 7)3rd NPT simulation with Parrinello-Rahman barostat (Ref. Pressure = 1 bar) having the following results : Statistics over 50001 steps [ 0. through 100. ps ], 1 data sets All statistics are over 10001 points Energy Average Err.Est. RMSD Tot-Drift - Pressure2.039590.995.9974 -6.788 (bar) All statistics are over 10001 points Energy Average Err.Est. RMSD Tot-Drift --- Density 1012.8 0.151.60294 0.243262 (kg/m^3) All the NPT equilibrations are of 100 ps and are continued from the previous equilibration. I observe that the average pressure has not yet reached the reference pressure and in the 3rd NPT run the Err.Est. , RMSD and Drift has increased. I have gone through the different comments and suggestions to my earlier posts. I am thinking of a 500 ps or 1 ns run with the Parinello Rahman barostat. Or am I failing to understand the physical significance of these average values and should have stopped after the 2nd NPT equilibration ? em_potential.png https://docs.google.com/file/d/0B-U8uULVZjfRZ0xfZGVrLVRYQVU/edit?usp=drive_web npt1_density.png https://docs.google.com/file/d/0B-U8uULVZjfRYUpKeGZfenNqRnM/edit?usp=drive_web npt1_pressure.png https://docs.google.com/file/d/0B-U8uULVZjfRa1FSWkNCTkxkM28/edit?usp=drive_web npt1_temp.png https://docs.google.com/file/d/0B-U8uULVZjfRcmFmdHBybjZRTnM/edit?usp=drive_web npt2density.png https://docs.google.com/file/d/0B-U8uULVZjfRaUZKa1JJNWJCcU0/edit?usp=drive_web npt2_pressure.png https://docs.google.com/file/d/0B-U8uULVZjfRTng2eW1iQUxPamc/edit?usp=drive_web npt3_density.png https://docs.google.com/file/d/0B-U8uULVZjfRUGJSQU9MRnhlUTQ/edit?usp=drive_web npt3_pressure.png https://docs.google.com/file/d/0B-U8uULVZjfRcXFJZkt3N1YtdzQ/edit?usp=drive_web nvt_temp.png https://docs.google.com/file/d/0B-U8uULVZjfRLTNNcmlEcFNSWDg/edit?usp=drive_web nvt_totalenergy.png https://docs.google.com/file/d/0B-U8uULVZjfRNFBZd05kMXNoYW8/edit?usp=drive_web Could anybody suggest why the reference pressure is not being reached ? Pressure is incredibly noisy, and you're going to get a distribution of values that varies wildly. Think generally about the statistics: if you were given three averages and standard deviations of -5.5 ± 85, -0.3 ± 93, and 2.0 ± 96, would you be able to say that they are significantly different from 1? Of course, you can do that analysis, but it's pretty clear that they're not. I have only seen an average pressure come out to 1.0 probably once so far in my career, though unfortunately (?) it is the case with one of my tutorials, so now everyone expects it to always happen :) Net result: your results are fine. Maybe over very long time periods you'll get to 1.0 or very close to it, but there is nothing wrong with your simulations and you're getting what you should be. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II,
Re: [gmx-users] connecting two chains
On 11/2/14 5:02 AM, Somayeh Alimohammadi wrote: Dear gmx users I am performing a simulation protein- ligand by gromacs. this protein contain two chains (A B) which separated from eachother. I did the following steps for pdb file 1- pdb2gmx –ignh –f initial.pdb –o initial.pdb –p topol.top -ter 2- editconf -bt cubic –f initial.pdb –o initial.pdb -c –d 0.9 3- genbox –cp initial.pdb –cs spc216.gro –o initial-box.pdb –p topol.top 4- grompp –f em.mdp –c initialbox.pdb –p topol.top –o xion.tpr 5- genion -s xion.tpr -o initial_ions.gro -p topol.top -pname NA -nname CL -nn (number of charge) everything was perfect, but the final pdb file has a problem which two chains are connected eachother. I would like to know how to solve these problems? If the two chains have unique chain identifiers in the starting .pdb file, and you don't use pdb2gmx -merge to create any sort of inter-molecular disulfides or anything, the chains are not connected. If there are bonds showing up in VMD or something, those usually aren't real because VMD isn't always smart. If there is something else going on, please provide evidence of what you mean (topology output or whatever else). -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Energy minimization of an UNKNOWN molecule.
Dear all, I am trying to run a gromacs simulation using an .itp file of an unknown molecule ( non protein and DNA). I don't want to put the .itp file in a forcefield folder and I would like put it in my working directory. Can you please tell me, what is procedure to finish the energy minimization? Please help me.. Thanks in advance, Kalyanashis -- Kalyanashis Jana email: kalyan.chem...@gmail.com -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Energy minimization of an UNKNOWN molecule.
just put the itp file in your working directory, and include it in the top file of your system, so that Gromacs can find it. Hope this helps. Victor 2014-11-02 8:54 GMT-06:00 Kalyanashis Jana kalyan.chem...@gmail.com: Dear all, I am trying to run a gromacs simulation using an .itp file of an unknown molecule ( non protein and DNA). I don't want to put the .itp file in a forcefield folder and I would like put it in my working directory. Can you please tell me, what is procedure to finish the energy minimization? Please help me.. Thanks in advance, Kalyanashis -- Kalyanashis Jana email: kalyan.chem...@gmail.com -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Energy minimization of an UNKNOWN molecule.
Thank you so much... I have tried to run the grompp step according to you. But it is showing Fatal error: Syntax error - File A-T.itp, line 7 Last line read: '[ atomtypes ] ' Invalid order for directive atomtypes I have attached the .itp file and .top file. Please kindly tell me, what to do now.. On Sun, Nov 2, 2014 at 9:15 PM, Victor Rosas Garcia rosas.vic...@gmail.com wrote: just put the itp file in your working directory, and include it in the top file of your system, so that Gromacs can find it. Hope this helps. Victor 2014-11-02 8:54 GMT-06:00 Kalyanashis Jana kalyan.chem...@gmail.com: Dear all, I am trying to run a gromacs simulation using an .itp file of an unknown molecule ( non protein and DNA). I don't want to put the .itp file in a forcefield folder and I would like put it in my working directory. Can you please tell me, what is procedure to finish the energy minimization? Please help me.. Thanks in advance, Kalyanashis -- Kalyanashis Jana email: kalyan.chem...@gmail.com -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Kalyanashis Jana email: kalyan.chem...@gmail.com -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Re : NPT Simulation average pressure lower than Reference set pressure
Pressure is incredibly noisy, and you're going to get a distribution of values that varies wildly. Think generally about the statistics: if you were given three averages and standard deviations of -5.5 ± 85, -0.3 ± 93, and 2.0 ± 96, would you be able to say that they are significantly different from 1? That really depends on the number of statistically independent observations in the samples. Without those numbers, the question is pretty much meaningless from the point of view of statistics. In a simulation of 100 ps the number of uncorrelated frames is pretty low. Cheers, Tsjerk -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Energy minimization of an UNKNOWN molecule.
On 11/2/14 11:32 AM, Kalyanashis Jana wrote: Thank you so much... I have tried to run the grompp step according to you. But it is showing Fatal error: Syntax error - File A-T.itp, line 7 Last line read: '[ atomtypes ]' Invalid order for directive atomtypes I have attached the .itp file and .top file. Please kindly tell me, what to do now.. Force-field level directives must be declared before molecule-level directives. So if your ligand requires new bonded or nonbonded parameters, or new atom types, it must be #included before the declaration of any [moleculetype]. So put your #include statement for the ligand topology immediately after the #include statement for the parent force field. -Justin On Sun, Nov 2, 2014 at 9:15 PM, Victor Rosas Garcia rosas.vic...@gmail.com wrote: just put the itp file in your working directory, and include it in the top file of your system, so that Gromacs can find it. Hope this helps. Victor 2014-11-02 8:54 GMT-06:00 Kalyanashis Jana kalyan.chem...@gmail.com: Dear all, I am trying to run a gromacs simulation using an .itp file of an unknown molecule ( non protein and DNA). I don't want to put the .itp file in a forcefield folder and I would like put it in my working directory. Can you please tell me, what is procedure to finish the energy minimization? Please help me.. Thanks in advance, Kalyanashis -- Kalyanashis Jana email: kalyan.chem...@gmail.com -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] problems with testing a new gromacs installation (my
hello, because nobody was able or wants to help me, i have to help myself. the solution was that cygwin doesnt work correctly with th newest version of the gcc compiler (4.9.0.1) integrated. i have to install cygwin with the gcc compiler version 4.8.3.3 and lo and behold, all tests passsed correctly. it costs me the whole weekend to check that. best regards hans -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] How to overcome the error Atom P in residue DC 3 was not found in the rtp entry DC5 with 28 atoms while sorting atom.
Dear gromacs users I have been tried to simulate the protein-dna complex. I got error as Atom P in residue DC 3 was not found in the rtp entry DC5 with 28 atoms while sorting atom upon using the command pdb2gmx. I have been added the P atom and bonds of P in the .rtp file which is the part of AMBER99SB-ILDN force field. After the modification of the dna.rtp file I also got the same error which mentioned above. Kindly tell me how to overcome this error. Thanks in advance Surya Graduate Student, India. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Simulating Multiple Solute Particles
Sorry everybody, I accidentally unsubscribed from the mailing list and missed my last response. Dr. Lemkul posted a message but I can't reply directly to it, so here's what he said: Your topology is constructed incorrectly, but without seeing it in its entirety, it is impossible to say. Please post the file for download somewhere and provide a link, otherwise copy and paste its entire contents into a reply if the message will be small enough. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul Thank you Justin! I think it's easier to just paste it here. This is my topol.top file: [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 2 yes 0.5 0.5 [ atomtypes ] ;name at.num mass charge ptype sigma epsilon CH3 15 15.035000.000 A 0.39100 0.66944 ;united atom Methyl [C-CH3] C 12 12.011000.000 A 0.35000 0.27614 ;C [R3CCOO-] (first carbon) CM 12 12.011000.000 A 0.37500 0.43932 ;carboxyl C [R-(C=O)-OH] O8 15.999400.000 A 0.30800 0.71128 ;carboxyl O [C-O-H] OM8 15.999400.000 A 0.29600 0.87864 ;carbonyl O [C=O] H11.007940.000 A 0.0 0.0 ;carboxyl H [C-O-H] OW8 15.999400.000 A 0.31660 0.65000 HW11.007940.000 A 0.0 0.0 [ moleculetype ] ; Namenrexcl TETR3 [ atoms ] ; nrtype resnr residuatomcgnr charge mass 1 CH3 1TETR C1 1 0 15.03500 2 C 1TETR C2 1 0 12.01100 3 C 1TETR C3 1 0 12.01100 4 CM 1TETR C4 1 0.38 12.01100 5 OM 1TETR O1 1 -0.38 15.99940 6 O 1TETR O2 1 -0.40 15.99940 7 H 1TETR H4 1 0.401.00794 [constraints] ; i j funct distance 1 2 10.14550 2 3 10.11780 3 4 10.14420 4 5 10.12040 4 6 10.13100 6 7 10.89000 ; Include SPC water topology #include oplsaa.ff/tip3p.itp [ system ] Tetrolic Acid in water [ molecules ] Tetrolic Acid500 SOL 5481 I made the file myself, so I hope I didn't make any syntax errors. I discovered with the .gro file that the spacing is very important since gromacs doesn't use delimiters but allows only a fixed number of characters for each entry. Is the .top file the same way? I just used a template from some example file and tried to make the numbers fit appropriately under the headings. If it's not correct, why didn't gromacs complain when I solvated it? Doesn't it read in the topology file then as well? I'm subscribed again so I won't miss a reply. Thanks again for the guidance! N. H. - Original Message - From: Nathan K Houtz nho...@purdue.edu To: gmx-us...@gromacs.org Sent: Sunday, October 26, 2014 10:49:35 PM Subject: Re: [gmx-users] Simulating Multiple Solute Particles Thanks for your help. And actually my version of gromacs does not have genbox anymore. (http://www.gromacs.org/Documentation/How-tos/Tool_Changes_for_5.0 at the bottom: GENBOX - This tool has been split to gmx solvate and gmx insert-molecules.) But it's no big deal, insert-molecules seemed to work just fine! Here are the commands I used: gmx insert-molecules -f tetrolic_acid.gro -ci tetrolic_acid.gro -nmol 499 -o tetrolic500.gro gmx solvate -cp tetrolic500.gro -cs spc216.gro -o tetrolic_solv.gro -p topol.top where tetrolic_acid.gro and topol.top are files I created myself to define the molecule. I checked the output in vmd and it looks like exactly what I want. But now I'm stuck on another step and I get a confusing error. I tried to minimize the energy via: gmx grompp -f minim.mdp -c tetrolic_solv.gro -p topol.top -o em.tpr I stole the minim.mdp file from a tutorial (http://bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/Files/minim.mdp). I don't know how to properly create an mdp file from scratch, but judging from the comments, it seems reasonable and I don't see anything that must be specific to the case in the tutorial. Anyway, I don't think it caused my error. The output for that
Re: [gmx-users] Energy minimization of an UNKNOWN molecule.
Thank you very much... But I am not going to use any parent molecules like protein or DNA. I would like to perform the gromacs simulation for this unknown molecule. First few lines of my topology file.. ; ; File 'topol.top' was generated ; By user: kollan (506) ; On host: master.localdomain ; At date: Sun Nov 2 20:28:10 2014 ; ; This is a standalone topology file ; ; It was generated using program: ; pdb2gmx - VERSION 4.6.3 ; ; Command line was: ; pdb2gmx -f A-T.pdb -o A-T1.pdb -p topol.top ; ; Force field was read from the standard Gromacs share directory. ; ; Include forcefield parameters # include A-T.itp ; ; Built itp for A-T.mol2 ;by user vzoete Mon Oct 27 06:32:46 CET 2014 ; ; [ atomtypes ] The yellow colored lines are first seven line A-T.itp file And the error was Fatal error: Syntax error - File A-T.itp, line 7 Last line read: '[ atomtypes ]' Invalid order for directive atomtypes Please help me.. On Mon, Nov 3, 2014 at 1:28 AM, Justin Lemkul jalem...@vt.edu wrote: On 11/2/14 11:32 AM, Kalyanashis Jana wrote: Thank you so much... I have tried to run the grompp step according to you. But it is showing Fatal error: Syntax error - File A-T.itp, line 7 Last line read: '[ atomtypes ]' Invalid order for directive atomtypes I have attached the .itp file and .top file. Please kindly tell me, what to do now.. Force-field level directives must be declared before molecule-level directives. So if your ligand requires new bonded or nonbonded parameters, or new atom types, it must be #included before the declaration of any [moleculetype]. So put your #include statement for the ligand topology immediately after the #include statement for the parent force field. -Justin On Sun, Nov 2, 2014 at 9:15 PM, Victor Rosas Garcia rosas.vic...@gmail.com wrote: just put the itp file in your working directory, and include it in the top file of your system, so that Gromacs can find it. Hope this helps. Victor 2014-11-02 8:54 GMT-06:00 Kalyanashis Jana kalyan.chem...@gmail.com: Dear all, I am trying to run a gromacs simulation using an .itp file of an unknown molecule ( non protein and DNA). I don't want to put the .itp file in a forcefield folder and I would like put it in my working directory. Can you please tell me, what is procedure to finish the energy minimization? Please help me.. Thanks in advance, Kalyanashis -- Kalyanashis Jana email: kalyan.chem...@gmail.com -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Kalyanashis Jana email: kalyan.chem...@gmail.com -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
