[gmx-users] effect of slab geometry correction on Coulomb energies for interface systems
Hi all, I am trying to investigate how the slab geometry correction affects calculated Coulomb energies for interface systems. I have an air/water interface with a box size of 3x3x9 nm. I ran 2 independent simulations with changing ewald_geometry option: 3d (default value), and 3dc. You can find short and reciprocal Coulomb energies below: *3d 3dc * short-range Coulomb -45260.2 (6.5) -45258.4 (5) Reciprocal Coulomb -3325.72 (0.13) -3325.54 (0.1) I am wondering why short-range and reciprocal Coulomb energies are the same within the error bars even though I use different schemes for ewald_geometry? Regards -- Ozge Engin- PhD candidate Koc University, College of Engineering Dept. of Computational Sciences Engineering Rumelifeneri Yolu, 34450 Sariyer/Istanbul, Turkey Email: ozge.en...@gmail.com, ozen...@ku.edu.tr Phone:+90-212-338-1542 Fax: +90-212-338-1548 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] problem with g_density
Hi all, I have some difficulties with understanding the output of g_density command. I have a system composed of two Lennard Jones particles, A and B in a 20.712x20.712x20.712 simulation box. The parameters between the two particles are given such that they do not mix, but they undergo a phase separation. I want to investigate the density profile of the system, and I used the following command line to do that: g_density -f traj.xtc -n index.ndx -dens number -sl 100 The density profile for the two types of particles looks OK except the boundaries of the simulation box. I mean I would not expect to get a number other than 0 at the lower and upper boundaries. I have also searched the mailing list. There was an e-mail similar to that one, but it was not replied. I have attached the density profile in the attachment. Why is it the case? Regards -- Ozge Engin dens.xvg Description: Binary data -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Different hexane/water surface tensions fo r different ensembles (NVT and NAɣT)
Hi all, I am trying to calculate the surface tension of hexane/water interface. I used two different ensembles: constant particle, volume, temperature (NVT), and constant area but let the box fluctuate on the z axis (NAɣT). Everything except the ensemble is the same for two simulation set-up s: number of molecules, temperature, temperature coupling, electrostatic and VDW interaction schemes, cut-off etc. I found a value close to the experimental one (52 dyn/cm) by using the NVT ensemble. In order to check whether it is dependent on the system size, I tried different sized systems, but it does not change. The results were the same within the error bars, which is good. However, when I attempt to change the ensemble to NAɣT I found different result. It is around 48 (1) dyn/cm. Actually, I expected to have the same values with the two ensembles, but not. Am I missing something that is straightforward? Regards -- Ozge Engin ★☆ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] information regarding the bootstrap method implemented with the g_wham
Hi all, I am trying to understand how the bootstrap method has been implemented within the g_wham. Unfortunately, it is poorly documented in the help menu and in the manual. I could not track of the options regarding the method. Could anyone (maybe the one who has implemented the method) give a little bit detailed information, please? Thanks in advance -- Ozge Engin ★☆ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] output of the -hist option of the g_wham command
Hi all, I am trying to perform umbrella sampling along with the WHAM to get the PMF. I go over the umbrella sampling tutorial prepared by Justin. Everything seems OK to me except one point. I could not understand the output given by the hist option of the g_wham command. There, what does histogram of configurations mean? Thank you -- Ozge Engin ★☆ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] number of water molecules affects the PMF
Hi Chris, The two setups were different from each other in terms of only the number of water molecules. Even the starting conformations for the two peptides were the same. I especially took care about that to leave only the number of molecules as a variable. I calculated the error by dividing the whole data to 4, and calculated the standard deviation between the 4 sets, and divided the result by sqrt (3). For the Xavier's suggestion: I think I should wait a little, at least until having the same length of trajectory for the two sets. Thanks -- Ozge Engin ★☆ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] number of water molecules affects the PMF
Hi all, I am trying to calculate the potential of mean force between the two hydrophobic dipeptides (phenylalanine) in bulk water via constraint pulling simulations. First, I calculated the mean force at each of the constraint points, and then I integrated the mean force curve to get the PMF. In order to test how big the effect of the number of water molecules on the calculated PMF I performed two sets of simulations which differed from each other in terms of only the number of water molecules. I used 9000 water molecules in one set, and 7000 in the other. The overall PMF for the latter was steeper than the former, as I expected before. However, the minimum point for the former was around 2.79 kJ/mol, and for the latter 5.30 kJ/mol. I did not think that the difference should not be that much since there is not a big difference between the number of water molecules between the two sets. I searched the internet to find a study regarding the concentration dependency of the PMF. Is this reasonable? Any suggestions? Regards Ozge Engin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: gmx-users Digest, Vol 74, Issue 13
Hi Xavier, Ok, it would be better to talk with the average values together with the corresponding error bars. For the system having smaller number of water molecules the minimum of the PMF was around -4.31+-0.97 kJ/mol, and for the other system it was around -1.75+-1.05 kJ/mol. Therefore, the difference is significant. Regards On Tue, Jun 1, 2010 at 11:30 PM, gmx-users-requ...@gromacs.org wrote: Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to gmx-users-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@gromacs.org When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. Re: number of water molecules affects the PMF (XAvier Periole) 2. Re: Fatal error: Atom O in residue CO 1 not found in rtp entry with 3 atoms while sorting atoms (Nilesh Dhumal) 3. Re: Fatal error: Atom O in residue CO 1 not found in rtp entry with 3 atoms while sorting atoms (Justin A. Lemkul) 4. Re: Fatal error: Atom O in residue CO 1 not found in rtp entry with 3 atoms while sorting atoms (Mark Abraham) -- Message: 1 Date: Tue, 1 Jun 2010 21:41:42 +0200 From: XAvier Periole x.peri...@rug.nl Subject: Re: [gmx-users] number of water molecules affects the PMF To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 92b14805-6abd-4d17-af3d-e6c88393d...@rug.nl Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes On Jun 1, 2010, at 9:13 PM, Ozge Engin wrote: Hi all, I am trying to calculate the potential of mean force between the two hydrophobic dipeptides (phenylalanine) in bulk water via constraint pulling simulations. First, I calculated the mean force at each of the constraint points, and then I integrated the mean force curve to get the PMF. In order to test how big the effect of the number of water molecules on the calculated PMF I performed two sets of simulations which differed from each other in terms of only the number of water molecules. I used 9000 water molecules in one set, and 7000 in the other. The overall PMF for the latter was steeper than the former, as I expected before. However, the minimum point for the former was around 2.79 kJ/mol, and for the latter 5.30 kJ/mol. I did not think that the difference should not be that much since there is not a big difference between the number of water molecules between the two sets. Could it be that the difference is within the error ? What happens if you cut your data of each simulation in two pieces? In other words are you converged? I searched the internet to find a study regarding the concentration dependency of the PMF. Is this reasonable? Any suggestions? Regards Ozge Engin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Message: 2 Date: Tue, 1 Jun 2010 15:42:22 -0400 From: Nilesh Dhumal ndhu...@andrew.cmu.edu Subject: Re: [gmx-users] Fatal error: Atom O in residue CO 1 not found in rtp entry with 3 atoms while sorting atoms To: jalem...@vt.edu,Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4d7dd068352ed48ab70927d368ba8ab6.squir...@webmail.andrew.cmu.edu Content-Type: text/plain;charset=iso-8859-1 I have addes the CO residue. Coordinate file REMARK Accelrys Discovery Studio PDB file REMARK Created: Fri May 28 17:26:23 Eastern Daylight Time 2010 HETATM1 C1 CO 0 -1.044 -0.027 0.066 0.00 0.00 C HETATM2 O2 CO 0 -0.009 0.642 -0.037 0.00 0.00 O HETATM3 O3 CO 0 -2.286 0.595 -0.030 0.00 0.00 O END in ffopla.rtp file. [ CO ] ; mandatory [ ATOMS ] ; mandatory C1 opls_9741.00 1 O2 opls_975 -0.50 2 O3 opls_976 -0.50 2 [ bonds ] C1 O2 C1 O3 I have also addes new atoms typs in ffopls.atp file. NIlesh On Tue, June 1, 2010 3:35 pm, Justin A. Lemkul wrote: Nilesh Dhumal wrote: Hello, I am getting the following error during pdb2gmx. Fatal error: Atom O in residue CO 1 not found in rtp entry with 3 atoms while sorting atoms I checked the pdb file and ffopls.rtp file also. And what did you find? To my knowledge there is no such residue CO in the ffoplsaa.rtp file
[gmx-users] g_sas command with the -q option
Hi all, I have a system which is composed of hexane-peptide-water-peptide-hexane layers. There, I selected the hexane+peptide system as the calculation group, and the hexane group as the output group to calculate the hexane area that is in contact with water. To do this I used the g_sas command with the -q option. I looked at the connelly.pdb file via vmd. I think the calculation and the output groups are shown in that file. I saw that the the upper, right and left sides of the simulation box have been included which means to me the periodic boundaries are not taken into account during the calculation. In addition, when I use the g_sas command I get a warning as the following: WARNING: Analysis based on vacuum simulations (with the possibility of evaporation)will certainly crash the analysis. Turning off pbc. So, the periodic boundary is taken into account or not during the sas calculation? Regards -- Ozge Engin ★☆ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: gmx-users Digest, Vol 72, Issue 36
rcoulomb = 1.2 ; Dielectric constant (DC) for cut-off or DC of reaction field epsilon-r = 1 ; Method for doing Van der Waals vdw-type = switch ; cut-off lengths rvdw-switch = 1 rvdw = 1.2 then i get the message :Maximum force: 3.14171e+03 Maximum force probably not small enough to ensure that you are in an energy well. Be aware that negative eigenvalues may occur when the resulting matrix is diagonalized. I am sorry to post such a lengthy query, but I have no clue about the root of the problem. Any suggestion will be of great help. Thanks in advance, Sarbani. -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20100408/a584f68b/attachment.html -- -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! End of gmx-users Digest, Vol 72, Issue 36 * -- Ozge Engin ★☆ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] problem with the energy minimization of a system composed of two NA+ ions and explicit water
Hi all, First of all, thank you for your quick reply Justin. Here, I want to state the problem in a clearer way. I have been trying to calculate the PMF between two NA+ ions in explicit water. In order to do that I first pulled one of the NA+ ions continuously with respect to the other until the farthest point on the PMF curve was reached. After that I split the continuous pulling trajectory from the points that are in correspondence with the constraint points of the PMF curve. These were done via *genera_start_4* script. I took each starting conformation, that was obtained from continuous pulling, solvated with water, and then energy minimized. Then, I prepared the systems for constraint pulling MD production runs. These were done via * input* script. Interestingly, systems (ion+water) at some of the constraint points could not been energy minimized, it reached to the machine epsilon, but not to the desired criteria. The force per atom was too high, around the order of ^4. Moreover, this issue was not distance-dependent, which means that the energy minimization worked for smaller constraint points, but not for some of the larger constraint points. When I looked at the problematic trajectories, I saw that bonds of a water molecule near the box boundary was longer. I thought that this may be due to genbox command. Because of the small radius of NA+ ion it may not check the overlaps among the atoms. In order to test whether it is the case I increased the LJ parameters of the ion. This worked for some of the points, but not for others. (Note that the diameter is still smaller than the constraint distance between the two ions.) I use ffG45a3 force field, and the scripts given above. I tried this with different versions of Gromacs: 4.0.7, 4.0.5, and faced with similar problems. Kind Regards -- Ozge Engin ★☆ genera_start_4 Description: Binary data input Description: Binary data -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] energy minimization of a box containing two Na+ ions and water does not converge
Hi all, I have been trying to calculate the PMF of two NA+ ions in explicit bulk water. First, I tried to calculate the mean force between the two ions at a distance of 0.48 nm, which is big enough than the diameter of the ions. I first energy minimized the system with the script below, but it did not converge. After that, I removed one of the ions, and tried again, it did not work again. I am using ffG43a1 ff, and checked whether I used the correct naming for the ion: Everything seems to be OK. I could not attach the initial coordinate file due to the limited size. If you want I can also sent it to you as well. *Script: * title = Minimization cpp = /usr/bin/cpp define = -DFLEX_SPC constraints = none integrator = steep dt = 0.002; ps ! nsteps = 3 nstlist = 10 ns_type = grid rlist = 1.0 vdwtype = cut-off coulombtype = PME rcoulomb= 1.0 rvdw= 1.4 fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes ; ; Energy minimizing stuff ; emtol = 100.0 emstep = 0.01 *Output*: Steepest Descents converged to machine precision in 36 steps, but did not reach the requested Fmax 100. Potential Energy = -1.0409969e+05 Maximum force = 9.6685031e+04 on atom 294 Norm of force = 1.4924829e+03 What may be the problem? Best Regards -- Ozge Engin ★☆ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] problem with the translate option of editconf
Hi all, I am trying to translate the peptide within the simulation box. I have a box with dimensions of 3.8 3.0 3.0 nm^3, and I want to put the peptide on top of the box. In order to that I used the following command line: editconf -f pep.pdb -box 3.8 3.0 3.0 -translate 0 0 1.5 -o trans.pdb The peptide is not translated, but sitting at the center of the box. Why is the case? Any suggestions? Thanks in advance -- Ozge Engin ★☆ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] coarse_grain.tcl script does not show all of the coarse-grained bonds in vmd
Hi all,
I was trying to show the bonds between my CG beads in VMD. I have four CG
beads per each molecule, and there are 18 separate molecules which contain
these four beads, which results in having 72 CG beads in total. Therefore,
I expect to see 54 CG bonds in the end.
I used the coarse_grain.tcl script to visualize these CG bonds as
suggested on the VMD page. I have two different bead types in the system: CA
and CG. In order to visualize the bonds I used the following command line on
Tk console:
source coarse_grained.tcl
g_cg -tpr topol.tpr -sel {{name CA} {name CB}} -rep {Licorice Licorice}
-color {name name}
After that it gave me the following lines:
[ g_cg ] Processing topol.tpr...
[ g_cg ] Create the bond list for 72 atoms...
[ g_cg ] Rebuild bonds...
[ g_cg ] Create representations...
which I understood that all the bonds are created successfully, but when I
looked at the screen I could see only one of those CG bonds, but not the
others. Why might be the reason?
Thanks in advance
--
Ozge Engin
★☆
--
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[gmx-users] Re: gmx-users Digest, Vol 68, Issue 21
Hi Nicholas, Sorry, I wrote the bead names wrong in the mail. I have just used the correct CG names, but could not see any bond other than one. Thank you On Thu, Dec 3, 2009 at 11:56 AM, gmx-users-requ...@gromacs.org wrote: Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to gmx-users-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@gromacs.org When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. Re: Pressure annealing in Gromacs? (Jussi Lehtola) 2. RE: Exclusions in topology file seem not working for big systems (Berk Hess) 3. coarse_grain.tcl script does not show all of the coarse-grained bonds in vmd (Ozge Engin) 4. Re: coarse_grain.tcl script does not show all of the coarse-grained bonds in vmd (Nicolas Sapay) -- Message: 1 Date: Thu, 03 Dec 2009 09:22:46 +0200 From: Jussi Lehtola jussi.leht...@helsinki.fi Subject: Re: [gmx-users] Pressure annealing in Gromacs? To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 1259824966.1913.1.ca...@politzer.theorphys.helsinki.fi Content-Type: text/plain; charset=UTF-8 On Thu, 2009-12-03 at 02:30 +1100, Mark Abraham wrote: Jussi Lehtola wrote: I'm experiencing trouble converging the density of some heavy liquid alcohols (after 10 ns of simulation the density is still changing linearly). Is there any way to run pressure annealing in Gromacs? Running the system through a high pressure and temperature might give an equilibrium structure quicker. There's nothing native that I'm aware of, but it should be straightforward to use sed or perl in a script to do the annealing by hand in a series of mdrun invocations. Yup, that came to mind but then one ends up with N trajectories and log files. And one has to run a big pile of grompp commands, that waste some parallel run time, so I really would like something integrated. Besides, a thing like changing the reference pressure should be a no-brainer in the source code - assuming the code is well structured and one knows it well beforehand. Anyway, the problem was solved for now already. Still, pressure annealing would be a nice addon to gromacs. (I'll open a bug on bugzilla about it.) -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto jussi.leht...@helsinki.fi, p. 191 50632 -- Mr. Jussi Lehtola, M. Sc., Doctoral Student Department of Physics, University of Helsinki, Finland jussi.leht...@helsinki.fi -- -- Message: 2 Date: Thu, 3 Dec 2009 09:30:27 +0100 From: Berk Hess g...@hotmail.com Subject: RE: [gmx-users] Exclusions in topology file seem not working for big systems To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: col113-w6464fde0d2532eb97fca938e...@phx.gbl Content-Type: text/plain; charset=iso-8859-1 Hi, If you really had too many exclusions you would get an error message. So I just tested this. I used the couple_moltype option to couple a 389 atom protein. This generates exclusions between each protein atom and the 388 others. All interactions are excluded correctly (and re-added as special 1-4's because of the couple option). So I don't understand what is going wrong in your case. Berk Date: Wed, 2 Dec 2009 09:31:03 -0800 From: resa...@yahoo.com Subject: Re: [gmx-users] Exclusions in topology file seem not working for big systems To: gmx-users@gromacs.org Thanks for your response Dr van der Spoel. Then there is a limit on the number of atoms that can be defined in the exclusions section. My smaller system has 60 atoms and I used exclusions successfully for that, so I guess the limit might be a little more than 32. Regarding the use of energygrp_excl,it seems it does not work with PME. If I define the protein in the energygrp_excl group, grompp gives me this warning: Can not exclude the lattice Coulomb energy between energy groups Which I think means some of electrostatics is not going to be excluded between protein atoms. Is there a workaround for this? I think my last resort would be to run a simulation first with PME and without exclusions, and then rerunning it but this time by defining protein in the energygrp_excl and using cut-off instead of PME. Then I guess I will be left with only protein-water interactions. Regards, Reza Salari From: David van der Spoel sp...@xray.bmc.uu.se
[gmx-users] error with pdb2gmx when using AMBER ff in GROMACS
Hi all, I am trying to use AMBER ff in GROMACS. I have followed the steps that are given in the http://chemistry.csulb.edu/ffamber/ link. The first residue of the protein is GLN. I put an N prefix to this residue. The pdg2gmx works well except giving an warning of long bond between some atoms. In contrast, if I have not put any prefix to GLN, then, the following error appears: +++ WARNING: atom H is missing in residue GLN 1 in the pdb file You might need to add atom H to the hydrogen database of residue GLN in the file ff???.hdb (see the manual) --- Program pdb2gmx, VERSION 3.3.1 Source code file: pdb2top.c, line: 697 Fatal error: There were 1 missing atoms in molecule Protein, if you want to use this incomplete topology anyhow, use the option -missing +++ I looked at both the .rtp and .hdb files, but everything seems to be correct. Does anybody face with a similar problem? Thanks in advance Ozge Engin = Computational Science Engineering Koc University ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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: Re: [gmx-users] error with pdb2gmx when using AMBER ff in GROMACS
I already indicated the problem that I have. If I put an N prefix to the first residue, I get warning of having long bonds. It has been indicated in the mail.Moreover, these long bonds can not be minimized during the minimization step. Although I put a relatively higher tolerance for the force on atoms. -Original Message- From: Justin A. Lemkul [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Mon, 31 Mar 2008 14:42:55 -0400 Subject: Re: [gmx-users] error with pdb2gmx when using AMBER ff in GROMACS Quoting OZGE ENGIN [EMAIL PROTECTED]: Hi all, I am trying to use AMBER ff in GROMACS. I have followed the steps that are given in the http://chemistry.csulb.edu/ffamber/ link. The first residue of the protein is GLN. I put an N prefix to this residue. The pdg2gmx works well except giving an warning of long bond between some atoms. In contrast, if I have not put any prefix to GLN, then, the following error appears: +++ WARNING: atom H is missing in residue GLN 1 in the pdb file You might need to add atom H to the hydrogen database of residue GLN in the file ff???.hdb (see the manual) --- Program pdb2gmx, VERSION 3.3.1 Source code file: pdb2top.c, line: 697 Fatal error: There were 1 missing atoms in molecule Protein, if you want to use this incomplete topology anyhow, use the option -missing +++ I looked at both the .rtp and .hdb files, but everything seems to be correct. Does anybody face with a similar problem? If it is an N-terminal residue, it needs to be preceded by an 'N' (i.e., NGLN), and likewise for C-terminal residues, CXXX. This is in the documentation from the AMBER ports at the link you cite above, and the link I already provided you. So what's the problem? -Justin Thanks in advance Ozge Engin = Computational Science Engineering Koc University ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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 Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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 Ozge Engin = Computational Science Engineering Koc University ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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: Re: Re: [gmx-users] error with pdb2gmx when using AMBER ff in GROMACS
Ok, it should be better to describe the problem in a more detailed way. I got this structure from Swiss-modeler program. I do not think I have a problem with the starting structure because I truncated the protein at some PRO residue, and got no error at all. So, there is something wrong about the nomenclature of the N terminus. I read things in the link, searched the web and made some discussion with my friend, but I could not find the source of the error :) Thank you Justin -Original Message- From: Justin A. Lemkul [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Mon, 31 Mar 2008 15:25:11 -0400 Subject: Re: Re: [gmx-users] error with pdb2gmx when using AMBER ff in GROMACS Quoting OZGE ENGIN [EMAIL PROTECTED]: I already indicated the problem that I have. If I put an N prefix to the first residue, I get warning of having long bonds. It has been indicated in the mail.Moreover, these long bonds can not be minimized during the minimization step. Although I put a relatively higher tolerance for the force on atoms. Alright, that makes more sense. You didn't say before that you couldn't resolve the long bonds by minimization. It seemed that you were asking again about the N-terminal nomenclature. It sounds like your starting structure has problems, but without knowing more I can't comment on that. Is it something you've built, something from the RCSB, etc? Have a look at your structure and the mdrun output (md.log, in particular) to see if you can determine where things are falling apart based on specific warnings (LINCS, etc.) -Justin -Original Message- From: Justin A. Lemkul [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Mon, 31 Mar 2008 14:42:55 -0400 Subject: Re: [gmx-users] error with pdb2gmx when using AMBER ff in GROMACS Quoting OZGE ENGIN [EMAIL PROTECTED]: Hi all, I am trying to use AMBER ff in GROMACS. I have followed the steps that are given in the http://chemistry.csulb.edu/ffamber/ link. The first residue of the protein is GLN. I put an N prefix to this residue. The pdg2gmx works well except giving an warning of long bond between some atoms. In contrast, if I have not put any prefix to GLN, then, the following error appears: +++ WARNING: atom H is missing in residue GLN 1 in the pdb file You might need to add atom H to the hydrogen database of residue GLN in the file ff???.hdb (see the manual) --- Program pdb2gmx, VERSION 3.3.1 Source code file: pdb2top.c, line: 697 Fatal error: There were 1 missing atoms in molecule Protein, if you want to use this incomplete topology anyhow, use the option -missing +++ I looked at both the .rtp and .hdb files, but everything seems to be correct. Does anybody face with a similar problem? If it is an N-terminal residue, it needs to be preceded by an 'N' (i.e., NGLN), and likewise for C-terminal residues, CXXX. This is in the documentation from the AMBER ports at the link you cite above, and the link I already provided you. So what's the problem? -Justin Thanks in advance Ozge Engin = Computational Science Engineering Koc University ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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 Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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 Ozge Engin = Computational Science Engineering Koc University ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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
Re: Re: Re: Re: [gmx-users] error with pdb2gmx when using AMBER ff in GROMACS
Justin, thank you very much for your attention. This is totally my fault. After putting N to the first residue, the column that indicates the coordinates has been flipped to the right. So, the first numbers could not be read by pdb2gmx. That is the source of the problem. However, thank you again. -Original Message- From: Justin A. Lemkul [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Mon, 31 Mar 2008 17:41:50 -0400 Subject: Re: Re: Re: [gmx-users] error with pdb2gmx when using AMBER ff in GROMACS Quoting OZGE ENGIN [EMAIL PROTECTED]: Ok, it should be better to describe the problem in a more detailed way. I got this structure from Swiss-modeler program. I do not think I have a problem with the starting structure because I truncated the protein at some PRO residue, and got no error at all. So, there is something wrong about the nomenclature of the N terminus. I read things in the link, searched the web and made some discussion with my friend, but I could not find the source of the error :) So have I got it correct that you truncated the N-terminus originally, and are now adding residues back? It still suggests to me that you've generated a poor starting structure; the nomenclature should not be causing the issue. Identify which bonds pdb2gmx is warning you about (and the atoms involved), and evaluate them with a viewer (VMD, etc). Likely the model you've constructed has some non-physical attributes. -Justin Thank you Justin -Original Message- From: Justin A. Lemkul [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Mon, 31 Mar 2008 15:25:11 -0400 Subject: Re: Re: [gmx-users] error with pdb2gmx when using AMBER ff in GROMACS Quoting OZGE ENGIN [EMAIL PROTECTED]: I already indicated the problem that I have. If I put an N prefix to the first residue, I get warning of having long bonds. It has been indicated in the mail.Moreover, these long bonds can not be minimized during the minimization step. Although I put a relatively higher tolerance for the force on atoms. Alright, that makes more sense. You didn't say before that you couldn't resolve the long bonds by minimization. It seemed that you were asking again about the N-terminal nomenclature. It sounds like your starting structure has problems, but without knowing more I can't comment on that. Is it something you've built, something from the RCSB, etc? Have a look at your structure and the mdrun output (md.log, in particular) to see if you can determine where things are falling apart based on specific warnings (LINCS, etc.) -Justin -Original Message- From: Justin A. Lemkul [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Mon, 31 Mar 2008 14:42:55 -0400 Subject: Re: [gmx-users] error with pdb2gmx when using AMBER ff in GROMACS Quoting OZGE ENGIN [EMAIL PROTECTED]: Hi all, I am trying to use AMBER ff in GROMACS. I have followed the steps that are given in the http://chemistry.csulb.edu/ffamber/ link. The first residue of the protein is GLN. I put an N prefix to this residue. The pdg2gmx works well except giving an warning of long bond between some atoms. In contrast, if I have not put any prefix to GLN, then, the following error appears: +++ WARNING: atom H is missing in residue GLN 1 in the pdb file You might need to add atom H to the hydrogen database of residue GLN in the file ff???.hdb (see the manual) --- Program pdb2gmx, VERSION 3.3.1 Source code file: pdb2top.c, line: 697 Fatal error: There were 1 missing atoms in molecule Protein, if you want to use this incomplete topology anyhow, use the option -missing +++ I looked at both the .rtp and .hdb files, but everything seems to be correct. Does anybody face with a similar problem? If it is an N-terminal residue, it needs to be preceded by an 'N' (i.e., NGLN), and likewise for C-terminal residues, CXXX. This is in the documentation from the AMBER ports at the link you cite above, and the link I already provided you. So what's the problem? -Justin Thanks in advance Ozge Engin = Computational Science Engineering Koc University ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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] residue names for AMBER ff in GROMACS
Hi all, I had a problem of converting of definition of residue names of AMBER96 ff in GROMACS package. Although I changed the residue names acc. to those defined in AMBER96 ff in my PDB file, I had the following error: (I have searched the mailing archieves for this error.) WARNING: atom H is missing in residue GLN 1 in the pdb fileYou might need to add atom H to the hydrogen database of residue GLN in the file ff???.hdb (see the manual). I looked at both .rtp and hdb files in order to investigate whether there are missing residues in these files, but the GLN residue name and the corresponding H names of this residue have been defined in .rtp and .hdb,respectively. So, what may be the problem? Thanks in advance Ozge Engin = Computational Science Engineering Koc University ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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] transfer of AMBER ion definitions to the ions.itp file
Hi all, I am trying to use AMBER96 ff under GROMACS package. I read the suggestions that were given at http://chemistry.csulb.edu/ffamber/. It has been stated that if any ion-related GROMACS tools will be used, then the AMBER ion definition to the ions.itp file should be added. So, does it mean that, I will copy the ions definitions that were given in the ffamber96.rtp file to the ions.itp file? I am a little bit confused because the definition of ions in AMBER is completely different from those of OPLS and GROMOS ff. Thanks in advance Ozge Engin = Computational Science Engineering Koc University ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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: Re: [gmx-users] transfer of AMBER ion definitions to the ions.itp file
You are right, Justin. I simply incorporated the corresponding terms to the ions.itp file by relying on the definition types made for GROMOS and OPLS ffs. -Original Message- From: Justin A. Lemkul [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Sat, 29 Mar 2008 11:54:22 -0400 Subject: Re: [gmx-users] transfer of AMBER ion definitions to the ions.itp file Quoting OZGE ENGIN [EMAIL PROTECTED]: Hi all, I am trying to use AMBER96 ff under GROMACS package. I read the suggestions that were given at http://chemistry.csulb.edu/ffamber/. It has been stated that if any ion-related GROMACS tools will be used, then the AMBER ion definition to the ions.itp file should be added. So, does it mean that, I will copy the ions definitions that were given in the ffamber96.rtp file to the ions.itp file? I am a little bit confused because the definition of ions in AMBER is completely different from those of OPLS and GROMOS ff. I don't see how these definitions are completely different. Use either of these sections (OPLS or GROMOS) in ions.itp as a guide and add the appropriate sections for AMBER96. Using the OPLS definitions will be most directly analogous in terms of how the atom types are defined. -Justin Thanks in advance Ozge Engin = Computational Science Engineering Koc University ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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 Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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 Ozge Engin = Computational Science Engineering Koc University ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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] changing the time step with tpbconv
Hi all, I am performing an 80-ns simulation. During the optimization of the parameters that were used in this run, I had performed some small test simulations, and used short frequency values to write the velocities. Unfortunately, I did not change this value into a bigger one before starting the main (longer) simulation. Consequently, I want to change the time step and use tpbconv to restart. Is there any way to do that? Thanks in advance... Ozge Engin = Computational Science Engineering Koc University ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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: Re: [gmx-users] changing the time step with tpbconv
Thank you David, for your quick reply. However, I could not understand the reason why I have to turn on unconstrained_start option. -Original Message- From: David van der Spoel [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Fri, 21 Mar 2008 17:03:06 +0100 Subject: Re: [gmx-users] changing the time step with tpbconv OZGE ENGIN wrote: Hi all, I am performing an 80-ns simulation. During the optimization of the parameters that were used in this run, I had performed some small test simulations, and used short frequency values to write the velocities. Unfortunately, I did not change this value into a bigger one before starting the main (longer) simulation. Consequently, I want to change the time step and use tpbconv to restart. Is there any way to do that? not with tpbconv, but with grompp -t -e -s -o you can do the same (with a new mdp file where you have to turn on unconstrained_start and to turn off gen_vel). Thanks in advance... Ozge Engin = Computational Science Engineering Koc University ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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 -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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 Ozge Engin = Computational Science Engineering Koc University ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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] problem with grompp (that is used instead of tpbconv)
Hi David, I did what you suggested but encountered with a problem similar to one encountered by tpbconv command. I got the following error: Reading frame 4 time 8000.000 WARNING: Incomplete frame: nr 40397 time 8079.4 --- Program grompp, VERSION 3.3.1 Source code file: grompp.c, line: 542 Fatal error: Can not start from an incomplete frame Ozge Engin = Computational Science Engineering Koc University ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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] pbc on the xy direction
Hi all, I am performing an air/water interface simulation and I want to implement anisotropic pbc condition (pbc on the xy direction) to my system. I have searched the mailing-list but could not find an appropriate answer. In the manual, two options are given for -pbc (xyz and no) . How can I implement it to my system? I use Gromacs 3.3.1 version. Thanks in advance Ozge Engin = Computational Science Engineering Koc University ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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: Re: [gmx-users] procedure for creating an S-S bridge
Thank you Mark, but I am a little bit confused. In the link you sent to me, http://wiki.gromacs.org/index.php/specbond.dat, the disulphide bond is described in the specbond.dat file (in the first line). However, the following sentence is written under the given table: To describe new possible special bonds, such as disulfides, so that pdb2gmx can generate them for you, you should add new lines similar to these example lines, and update the counter in the first line. So, I understood that the description made within the table does not describe the Cys-Cys bond. Then, what does it represent? After I used the pdb2gmx with -ss option, the type of Cys is given as CYSH in the .gro file. So, which one is true? Additionaly, I think, this type of information is not enough to create a disulphide bond. My cysteine residues are not directed to each other for making a Cys-Cys bond. So, what types of steps do I have to follow ? There are papers, of course, in which these types of bonds are made, but the description is not made properly. Thanks in advance -Original Message- From: Mark Abraham [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Mon, 3 Mar 2008 10:15:48 +1100 (EST) Subject: Re: [gmx-users] procedure for creating an S-S bridge Hi all, I want to create an S-S bond within my peptide. So, I used the CYSH type cysteine residue and pdb2gmx with -ss option. However, I saw that the S-S bridge was formed between the ARG-CYS pair but not between the CYS-CYS pair. That's not possible with the unmodified form of specbond.dat - you are probably seeing a visualization artefact http://wiki.gromacs.org/index.php/Trajectory_Visualisation#Topology_bonds_vs_Rendered_bonds. So, I think -ss option with pdb2gmx is not enough to make this bond. What additional steps do I follow to construct this bond ? Check out http://wiki.gromacs.org/index.php/specbond.dat Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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 Ozge Engin = Computational Science Engineering Koc University ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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: Re: Re: [gmx-users] procedure for creating an S-S bridge
So, from the explanation made within table I understood that after selecting -ss option, I would see the type of cys as CYS2 in the constructed .gro file as well as in the .top file since the CYS2 name appears in the 8 th and 9 th columns and they are described as the new name for residue A and residue B. So, I should perform a preliminary simulation in order to make the corresponding cysteine residue within the cutoff? -Original Message- From: Mark Abraham [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Mon, 3 Mar 2008 20:46:15 +1100 (EST) Subject: Re: Re: [gmx-users] procedure for creating an S-S bridge Thank you Mark, but I am a little bit confused. In the link you sent to me, http://wiki.gromacs.org/index.php/specbond.dat, the disulphide bond is described in the specbond.dat file (in the first line). However, the following sentence is written under the given table: To describe new possible special bonds, such as disulfides, so that pdb2gmx can generate them for you, you should add new lines similar to these example lines, and update the counter in the first line. So, I understood that the description made within the table does not describe the Cys-Cys bond. Then, what does it represent? What do you think the second line of the file describes? After I used the pdb2gmx with -ss option, the type of Cys is given as CYSH in the .gro file. ... and the pdb2gmx output doesn't report making a special bond, and using pdb2gmx without the -ss option produces the same output. Your conclusion here is...? So, which one is true? Additionaly, I think, this type of information is not enough to create a disulphide bond. My cysteine residues are not directed to each other for making a Cys-Cys bond. So, what types of steps do I have to follow ? There are papers, of course, in which these types of bonds are made, but the description is not made properly. See the final line of the specbond.dat page. You'll need to change your input structure. Think about distance restraints and a preparatory MD simulation. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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 Ozge Engin = Computational Science Engineering Koc University ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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] incorporation of distance restraint into the topology file
Hi all, I have a question regarding the creating a disulphide bridge. If I want to impose a position restraint on this bond how can I incorporate it into the topology file? It is explained in the manual but the explanation for the last three columns is not clear. I could not decide to put what numbers into these columns. P.S: I use Gromacs 3.3.1 Thanks in advance Ozge Engin = Computational Science Engineering Koc University ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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: Re: [gmx-users] problem with exchange probabilities in remd
Thank you for your suggestions Mark and David. I have read papers you mentioned. Moreover, I also read the Berk Hess's paper in which the NPT NVT remd was compared (JMB 354/173-183). Since I have not a high T within my temperature distribution (the highest one is around 320K), there will be no large pressure input. In Berk's paper, it was stated that the fluctuation in volume is negligible in NPT simulation. However, due to the low density value at high T, the energy of the system will be high leading to a decrease in the overlapping of energy distribution as well as the exchange probabilities. I am looking forward to the implementation of NVT within the temperature generator :-) -Original Message- From: Mark Abraham [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Sun, 24 Feb 2008 13:34:51 +1100 Subject: Re: [gmx-users] problem with exchange probabilities in remd OZGE ENGIN wrote: Hi all, I am performing a remd simulation of a peptide+water system. I have tried different temperature distributions. I am using an NVT ensemble. My temperature coupling constant is 0.1 ps. The problem is that upon increasing the temperature difference between the two replicas more than two (290==294), the exchange probability decreases sharply, app. to 0.03. Yep. That's normal for decent-sized explicit-solvent REMD. You can choose a lowest temperature spacing that isn't an integer, of course. I have changed the exchange frequency in order to get a better exchange probabilities. However, it has not affected the overall exchange probabilities so much. The frequency is independent of the probability, at least until you get to periods so short that successive attempts are correlated. See Periole and Mark, J Chem Phys 126 014903, and for a counter-view, Sindhikara, Meng and Roitberg J Chem Phys 128 024103. Both frequency and probability affect the exchange acceptance rate, of course. Is there anybody who has encountered such a situation? Yep. Consider seriously how big a temperature range you might need. There's discussion out there that the increased-sampling effect of the increased temperature range is outweighed by the ability of the replicas to sort themselves as a function of T. See Periole paper above. Thus, there's no need to go to 800K, like you see implicit-solvent REMD achieve. 373K is enough to start denaturing proteins in cooking, after all :-) Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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 Ozge Engin = Computational Science Engineering Koc University ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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] which type of cysteine residue?
Hi all, I want to make the cysteine residues of my peptide to make a disulphide bridge with each other. So, what type of cysteine residue should I use? There are 4 possibilities. CYS, CYSH, CYS1, CYS2. The last two seems to be the same in respect of atomic charges, bond types but not parameters for dihedral angles. Thanks in advance Ozge Engin = Computational Science Engineering Koc University ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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] problem with exchange probabilities in remd
Hi all, I am performing a remd simulation of a peptide+water system. I have tried different temperature distributions. I am using an NVT ensemble. My temperature coupling constant is 0.1 ps. The problem is that upon increasing the temperature difference between the two replicas more than two (290==294), the exchange probability decreases sharply, app. to 0.03. I have changed the exchange frequency in order to get a better exchange probabilities. However, it has not affected the overall exchange probabilities so much. Is there anybody who has encountered such a situation? Thanks in advance Ozge Engin = Computational Science Engineering Koc University ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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: Re: [gmx-users] distance options for g_cluster
Thank you Mark for your feedbacks. There is one more point that is not clear to me for the output of g_cluster, In the second column of the cluster.log of g_cluster, the same rmsd values are indicated for different clusters. What does it mean? Although these clusters have the same cut-off value, they are grouped in different clusters, Why? Thank you. -Original Message- From: Mark Abraham [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Sun, 17 Feb 2008 22:35:20 +1100 Subject: Re: [gmx-users] distance options for g_cluster OZGE ENGIN wrote: Hi all, I am trying to understand what type of distance can be used with g_cluster? In the manual, it is written that RMS deviation after fitting or RMS deviation of atom-pair distances can be used to define the distance between structures in the first paragraph. However, in the other options part, two options are indicated for -dista option, which indicates the type of distance that will be used with g_cluster. They are RMSD of distances or RMS deviation. Consequently, the information in the first paragraph does not coincide with that given in the other options part for -dista option. Maybe I could not understand. Could anyone explain this in a clearer way, please? I agree that it is not very clear what is meant in the documentation, and I have wondered myself what it means. This is one of the reasons that the source code is made available. I had a quick look, and -dista yes looks like it implements the RMS deviation of atom-pair distances quoted above. That is, it forms an atom-pair distance matrix for each structure in the trajectory, and then does an all-against-all root-mean-square comparison of those matrices to generate the structure comparison matrix for clustering. You'd be well advised to verify that yourself. It's all in src/tools/gmx_cluster.c Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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 is made available. I had a quick look, and -dista yes looks like it implements the RMS deviation of atom-pair distances quoted above. That is, it forms an atom-pair distance matrix for each structure in the trajectory, and then does an all-against-all root-mean-square comparison of those Ozge Engin = Computational Science Engineering Koc University ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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] Stanford workshop april 7-8
Hi Erik, Did you put up a registration page for the workshop? Could you give information, if there is any, about the workshop that will be held in Göttingen? I am outside of the countries you mentioned :) -Original Message- From: Erik Lindahl [EMAIL PROTECTED] To: gmx-users@gromacs.org Date: Fri, 15 Feb 2008 20:13:19 +0100 Subject: [gmx-users] Stanford workshop april 7-8 Hi again, Quick update: I've finally settled the block room reservations at the guest house ($89 for singles, $119 for doubles), and will try to put up a registration page in a couple of hours. I think I have a solution to keep it reasonably fair just in case there's overwhelming interest: In the first round I'll simply let everybody register until tuesday night (PST) next week, and if by then there are more people than slots (~30) we will have to draw randomly, but give people from US/Canada/ Mexico priority. Hopefully Europeans will get another chance in Göttingen soon :-) From wednesday any possible remaining slots will be filled on a first- come, first-served, basis. Cheers, Erik Erik Lindahl [EMAIL PROTECTED] Backup: [EMAIL PROTECTED] Assistant Professor, Computational Structural Biology Center for Biomembrane Research, Dept. Biochemistry Biophysics Stockholm University, SE-106 91 Stockholm, Sweden Tel: +46(0)8164675 Mobile: +46(0)704218767 Fax: mail a PDF instead ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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 Ozge Engin = Computational Science Engineering Koc University ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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] distance options for g_cluster
Hi all, I am trying to understand what type of distance can be used with g_cluster? In the manual, it is written that RMS deviation after fitting or RMS deviation of atom-pair distances can be used to define the distance between structures in the first paragraph. However, in the other options part, two options are indicated for -dista option, which indicates the type of distance that will be used with g_cluster. They are RMSD of distances or RMS deviation. Consequently, the information in the first paragraph does not coincide with that given in the other options part for -dista option. Maybe I could not understand. Could anyone explain this in a clearer way, please? Thanks in advance Ozge Engin = Computational Science Engineering Koc University ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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: Re: Re: Re: [gmx-users] still got the problem with the output of g_cluster
Thank you very much Mark, it is clear to me now! -Original Message- From: [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Fri, 15 Feb 2008 18:44:51 +1100 Subject: Re: Re: Re: [gmx-users] still got the problem with the output of g_cluster So we're expecting a histogram of an all-against-all RMSD calculation over 3000-odd elements. So we should expect that around 3000*3000*0.5 entries exist in the histogram... that's about 450 entries. That sounds familiar, now :-) For 3002 elements, excluding self-comparisons, there are 3001-choose-2 combinations, i.e. 3001*3000*0.5, which is the number you give below. The values in this column are consistent with a histogram. Mark - Original Message - From: OZGE ENGIN [EMAIL PROTECTED] Date: Friday, February 15, 2008 6:32 pm Subject: Re: Re: Re: [gmx-users] still got the problem with the output of g_cluster To: gmx-users@gromacs.org Cc: gmx-users@gromacs.org Sorry Mark, the sum of the 2 nd column is 4501500. The frame number is 3002. -Original Message- From: [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Fri, 15 Feb 2008 10:04:45 +1100 Subject: Re: Re: [gmx-users] still got the problem with the output of g_cluster What's the sum of the second column? Mark - Original Message - From: OZGE ENGIN [EMAIL PROTECTED] Date: Friday, February 15, 2008 9:46 am Subject: Re: Re: [gmx-users] still got the problem with the output of g_cluster To: gmx-users@gromacs.org Hi Mark, You are right. While I am writing,most of the things in my mind are lost :) The actual command line is: g_cluster -s .tpr -f .xtc -dist and it gives a output file named rmsd-dist.xvg. In the first column, the rmsd values are written. However, I can not understand the values in the second column, the title of second column is only indicated. No explanation has been made in the manual. The frame number is 3000. One of the numbers on that column exceeds that value. -Original Message- From: Mark Abraham [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Fri, 15 Feb 2008 09:11:55 +1100 Subject: Re: [gmx-users] still got the problem with the output of g_cluster OZGE ENGIN wrote: Hi all, I have still got the problem with the second column of the output of g_cluster with -dist option. Xavier said that the a.u stands for arbitrary unit and I think it gives the histogram of rmsd value distribution. If so, I can not understand why the total of this column is not equal to the total number of conformations obtained from the simulation. Well, what is it equal to? How many frames are you using, what are your actual command lines? Can you provide a short excerpt of the .xvg file? Please consider the point of view of the people of whom you're asking such a question. Unless they're actually fluent with the code and useage of g_cluster, they don't have the answer at their fingertips. However if you give them useful information, they might be able to see things that you can't. If you don't provide useful information, then even users who do have the answer at their fingertips might decide you're not worth their time :-) Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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 Ozge Engin = Computational Science Engineering Koc University ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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 search the archive at http://www.gromacs.org/search before posting! 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 Ozge Engin = Computational Science Engineering Koc University ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users
[gmx-users] there is no enough information about the implementation of both diagonalization and Monte Carlo methods of g_cluster in the manual
Hi all, I have two questions about the g_cluster. 1) I want to test the performance of the clustering methods implemented in g_cluster. However, although there are some information about the gromos,Jarvis Patrick, and single linkage methods both in the manual and on the internet, there are no information about the implementation of both the Monte Carlo and the diagonalization method. I know that when diagonalizing a matrix, the eigenvalues are found, and then how they are used for the clustering? 2)There are two options for the -dista option of the g_cluster: rmsd of distance and RMS deviation. What is the difference between these two? One of them gives the absolute rmsd of each frame and the other gives the relative rmsd according to the average rmsd? Thanks in advance Ozge Engin = Computational Science Engineering Koc University ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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] rmsd distance and rmsd deviation option for the -dista option of g_cluster
Hi all, There are two options for the -dista option of the g_cluster: rmsd of distance and RMS deviation. What is the difference between these two? One of them gives the absolute rmsd of each frame and the other gives the relative rmsd according to the average rmsd? Thank you Ozge Engin = Computational Science Engineering Koc University ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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] still got the problem with the output of g_cluster
Hi all, I have still got the problem with the second column of the output of g_cluster with -dist option. Xavier said that the a.u stands for arbitrary unit and I think it gives the histogram of rmsd value distribution. If so, I can not understand why the total of this column is not equal to the total number of conformations obtained from the simulation. Thanks in advance Ozge Engin = Computational Science Engineering Koc University ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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: Re: [gmx-users] still got the problem with the output of g_cluster
Hi Mark, You are right. While I am writing,most of the things in my mind are lost :) The actual command line is: g_cluster -s .tpr -f .xtc -dist and it gives a output file named rmsd-dist.xvg. In the first column, the rmsd values are written. However, I can not understand the values in the second column, the title of second column is only indicated. No explanation has been made in the manual. The frame number is 3000. One of the numbers on that column exceeds that value. -Original Message- From: Mark Abraham [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Fri, 15 Feb 2008 09:11:55 +1100 Subject: Re: [gmx-users] still got the problem with the output of g_cluster OZGE ENGIN wrote: Hi all, I have still got the problem with the second column of the output of g_cluster with -dist option. Xavier said that the a.u stands for arbitrary unit and I think it gives the histogram of rmsd value distribution. If so, I can not understand why the total of this column is not equal to the total number of conformations obtained from the simulation. Well, what is it equal to? How many frames are you using, what are your actual command lines? Can you provide a short excerpt of the .xvg file? Please consider the point of view of the people of whom you're asking such a question. Unless they're actually fluent with the code and useage of g_cluster, they don't have the answer at their fingertips. However if you give them useful information, they might be able to see things that you can't. If you don't provide useful information, then even users who do have the answer at their fingertips might decide you're not worth their time :-) Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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 Ozge Engin = Computational Science Engineering Koc University ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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: Re: Re: [gmx-users] still got the problem with the output of g_cluster
Sorry Mark, the sum of the 2 nd column is 4501500. The frame number is 3002. -Original Message- From: [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Fri, 15 Feb 2008 10:04:45 +1100 Subject: Re: Re: [gmx-users] still got the problem with the output of g_cluster What's the sum of the second column? Mark - Original Message - From: OZGE ENGIN [EMAIL PROTECTED] Date: Friday, February 15, 2008 9:46 am Subject: Re: Re: [gmx-users] still got the problem with the output of g_cluster To: gmx-users@gromacs.org Hi Mark, You are right. While I am writing,most of the things in my mind are lost :) The actual command line is: g_cluster -s .tpr -f .xtc -dist and it gives a output file named rmsd-dist.xvg. In the first column, the rmsd values are written. However, I can not understand the values in the second column, the title of second column is only indicated. No explanation has been made in the manual. The frame number is 3000. One of the numbers on that column exceeds that value. -Original Message- From: Mark Abraham [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Fri, 15 Feb 2008 09:11:55 +1100 Subject: Re: [gmx-users] still got the problem with the output of g_cluster OZGE ENGIN wrote: Hi all, I have still got the problem with the second column of the output of g_cluster with -dist option. Xavier said that the a.u stands for arbitrary unit and I think it gives the histogram of rmsd value distribution. If so, I can not understand why the total of this column is not equal to the total number of conformations obtained from the simulation. Well, what is it equal to? How many frames are you using, what are your actual command lines? Can you provide a short excerpt of the .xvg file? Please consider the point of view of the people of whom you're asking such a question. Unless they're actually fluent with the code and useage of g_cluster, they don't have the answer at their fingertips. However if you give them useful information, they might be able to see things that you can't. If you don't provide useful information, then even users who do have the answer at their fingertips might decide you're not worth their time :-) Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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 Ozge Engin = Computational Science Engineering Koc University ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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 search the archive at http://www.gromacs.org/search before posting! 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 Ozge Engin = Computational Science Engineering Koc University ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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] the 2 nd column of the output of g_cluster with -dist option
Hi all, What does the second column of the output file of g_cluster with -dist option stand for? Its title is a.u. I think it is atomic unit? In the manual, it is not described. Thanks in advance Ozge Engin = Computational Science Engineering Koc University ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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: Re: [gmx-users] the 2 nd column of the output of g_cluster with -dist option
Xavier, The output file of g_cluster with -dist option then gives the histogram of rmsd value distribution, is it? If it is the case, after plotting these data,I observe that the distribution resembles a gaussian type, its mean is located around 0.4 nm. This value is bigger compared to yours. Is it feasible? I performed my remd simulation in vacuum. It may be the reason? -Original Message- From: Xavier Periole [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Tue, 12 Feb 2008 23:10:02 +0100 Subject: Re: [gmx-users] the 2 nd column of the output of g_cluster with -dist option On Tue, 12 Feb 2008 23:55:35 +0200 OZGE ENGIN [EMAIL PROTECTED] wrote: Hi all, What does the second column of the output file of g_cluster with -dist option stand for? Its title is a.u. I think it is atomic unit? In the manual, it is not described. I believe a.u. stands for arbitrary unit. It should be the normalized distribution. You can check by integrating the curve ... should be one. XAvier Thanks in advance Ozge Engin = Computational Science Engineering Koc University ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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 - XAvier Periole - PhD NMR Molecular Dynamics Group University of Groningen The Netherlands http://md.chem.rug.nl/~periole - ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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 Ozge Engin = Computational Science Engineering Koc University ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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] g_rms , getting rmsd matrix and the histogram of this matrix
Hi all, I have three questions. 1)In order to get the rmsd distribution of all the conformations, I used g_rmsd. In the help menu, it is stated that g_rmsd compares the structure given by -s and compares it to the others which are given by -f option. Consequently, I can not get the rmsd between all pairs of conformations. how can I get the rmsd between all of the pairs? 2)How can I get the rmsd matrix? In manual, it is indicated that with option -m, you produce a matrix. However, with xv, I can not see the matrix exactly. 3)Is there any specific tool for plotting the histogram of the rmsd matrix? Thanks in advance Ozge Engin = Computational Science Engineering Koc University ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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] exchanged pairs in the log file of a remd simulation
Hi all, I am performing replica exchange MD simulations. Here, I attach the part of a log file which gives info about the exchanges made at step 46000 and 47000. It is just a test run. As you can see, on the line 2, it is indicated that the exchange is made between the rep 1 and rep 2 or between the repl2 and repl3. The case is the same for other time steps. There are no other types of pairs. Why? Replica exchange at step 46000 time 92 Line 2: Repl 1 - 2 dE = 3.006e-01 Repl ex 01 x 23 x 45 x 67 x 89 x 10 11 x 12 13 Repl pr.74 1.0 1.0 .70 .40 1.0 Replica exchange at step 47000 time 94 Line 2: Repl 2 - 3 dE = 7.473e-01 Repl ex 0 x 1234 x 56 x 78 x 9 10 11 12 13 Repl pr .04 .47 1.0 1.0 .65 .60 .34 Thanks in advance Ozge Engin = Computational Science Engineering Koc University ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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: Re: [gmx-users] exchanged pairs in the log file of a remd simulation
Thank you for your answers! You are right, Mark. I looked at the md1.log file and when I looked at the others I saw that there were different pairs other than 1-2 and 2-3. Consequently, there is no problem then. All the pairs, providing their energies are overlapped sufficiently, are exchanged? Is it what is happening? -Original Message- From: Mark Abraham [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Sun, 3 Feb 2008 20:50:55 +1100 (EST) Subject: Re: [gmx-users] exchanged pairs in the log file of a remd simulation Hi all, I am performing replica exchange MD simulations. Here, I attach the part of a log file which gives info about the exchanges made at step 46000 and 47000. It is just a test run. As you can see, on the line 2, it is indicated that the exchange is made between the rep 1 and rep 2 or between the repl2 and repl3. The case is the same for other time steps. There are no other types of pairs. Why? Replica exchange at step 46000 time 92 Line 2: Repl 1 - 2 dE = 3.006e-01 Repl ex 01 x 23 x 45 x 67 x 89 x 10 11 x 12 13 Repl pr.74 1.0 1.0 .70 .40 1.0 Replica exchange at step 47000 time 94 Line 2: Repl 2 - 3 dE = 7.473e-01 Repl ex 0 x 1234 x 56 x 78 x 9 10 11 12 13 Repl pr .04 .47 1.0 1.0 .65 .60 .34 I'd guess that you're looking at your *_1.log and thus you're seeing the numbers for the successful exchanges for only this replica. In the GROMACS implementation, I guess that the potential energies are only swapped between current exchange pairs, and not distributed to the whole replica system. Thus different .log files will probably have different such lines, because only two of the replicas have the necessary information. Odd and even pairs are considered for exchange at alternate exchange attempts, of course, as described in the manual. The 'x' characters denote succesful exchanges, as you will see documented early on in the log file (e.g. grep ^Repl *.log) Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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 Ozge Engin = Computational Science Engineering Koc University ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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] Address for the server of a REMD temperature calculator
Hi all, Somebody has sent a mail which is about the address of a server in which the temperatures for a REMD simulation is calculated. However, I can not find this mail. Could you sent the address of the server, please? Thank you Ozge Engin = Computational Science Engineering Koc University ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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] Replica Exchange MD using Gromacs
Hi Monica, I had not found a detailed tutorial about it; however, you can search for papers in which the simulations are performed via REMD.This will be helpful. Ozge. -Original Message- From: Monika Sharma [EMAIL PROTECTED] To: gmx-users@gromacs.org Date: Fri, 30 Nov 2007 17:04:07 +0530 (IST) Subject: [gmx-users] Replica Exchange MD using Gromacs Dear All, I am trying REMD for the first time using Gromacs. But I am not finding any much helpful material regarding the replica exchange using Gromacs. Can anyone who has done REMD please let me know about any good tutorial where I can understand the way this replica exchange work in gromacs and the right protocol to do so.. Thanks a lot in advance.. Regards, Monika CCNSB, IIIT, Hyderabad. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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 search the archive at http://www.gromacs.org/search before posting! 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] The fifth column of the output file of g_sas command
Hi all, I have a question about the output file of g_sas. The fifth column corresponds to Solvation free energy. I selected the whole peptide for analyzing. It did not take negative value, but rather it took positive values. As it takes larger + values, it means that the peptide or group under consideration interacts with solvent (water) favorably? Thanks in advance Ozge. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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] Problem with replica exchange in vacuum
Hi all, I am performing a REMD simulation in vacuum. Although I minimized the energy of each initial replica by using a stringent convergence criterion, after the the third attempt, the system exploided because of a huge deviation in the Lincs algorithm. Although I started to the simulation via low-energy structures, what may be the probable reason for this? Is it because of vacuum? Thank you Ozge ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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] Problem with replica exchange in vacuum
Hi all, I am performing a REMD simulation in vacuum. Although I minimized the energy of each initial replica by using a stringent convergence criterion, after the the third attempt, the system exploided because of a huge deviation in the Lincs algorithm. Although I started to the simulation via low-energy structures, what may be the probable reason for this? Is it because of vacuum? Thank you Ozge ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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] Neutralizing the total charge of the system in vacuum
Hi all, I am performing a simulation in vacuum. The peptide has nonzero charge, so I attempted to neutralize the total charge via genion;however as it is known, it asks for a continuous group for replacing, but I have no solvent molecules for the replacement. How can I neutralize the total charge while performing simulations in vacuum? Thanks in advance Oz. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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: Re: RE: [gmx-users] problem with mdrun performing replica exchange MD
This time I used the following command line: mpirun -np 8 mdrun_mpi -s simul0.tpr -replex 2500 -reseed -1 -multi 8. I got the following error: Program mdrun_mpi, VERSION 3.3.99_development_20070413 Source code file: gmxfio.c, line: 706 Can not open file: simul0_md0.tpr --- Don't Eat That Yellow Snow (F. Zappa) Error on node 0, will try to stop all the nodes Halting parallel program mdrun_mpi on CPU 0 out of 8. I could not understand this error because I do not have such a file: simul0_md0.tpr. -Original Message- From: Berk Hess [EMAIL PROTECTED] To: gmx-users@gromacs.org Date: Fri, 23 Nov 2007 10:58:48 +0100 Subject: Re: RE: [gmx-users] problem with mdrun performing replica exchange MD You need to supply the -np option. In Gromacs 3.3 you don't need to set the -multi option, and -multi does not take an argument. If you use the CVS head branch, you need to set -np and -multi both with an argument. Berk. From: OZGE ENGIN [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: gmx-users@gromacs.org Subject: Re: RE: [gmx-users] problem with mdrun performing replica exchange MD Date: Fri, 23 Nov 2007 11:44:47 +0200 Hi Berk, I indicated the number of replicas with -multi option. In additon, I have compiled Gromacs with MPI support. I used the following command line: mdrun -s simul0.tpr -multi 16 -reseed -1 -replex 2500 -Original Message- From: Berk Hess [EMAIL PROTECTED] To: gmx-users@gromacs.org Date: Fri, 23 Nov 2007 10:36:57 +0100 Subject: RE: [gmx-users] problem with mdrun performing replica exchange MD From: OZGE ENGIN [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: gmx-users@gromacs.org Subject: [gmx-users] problem with mdrun performing replica exchange MD Date: Fri, 23 Nov 2007 11:30:53 +0200 Hi All, I am performing replica exchange molecular dynamics simulation(REMD). I have 16 replicas each of which has a peptide with different conformation. After obtaining .tpr files (at desired temperatures) for each replicas, I loaded them via mdrun, but I got the following error: Fatal error: Nothing to exchange with only one replica --- Why? I guess there are two possibilities. Or you did not use the -np option of mdrun to set the number of replicas, or you have not compiled Gromacs with MPI support. Berk. _ Talk with your online friends with Messenger http://www.join.msn.com/messenger/overview ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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 search the archive at http://www.gromacs.org/search before posting! 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 _ Play online games with your friends with Messenger http://www.join.msn.com/messenger/overview ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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 search the archive at http://www.gromacs.org/search before posting! 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] problem with mdrun performing replica exchange MD
Hi All, I am performing replica exchange molecular dynamics simulation(REMD). I have 16 replicas each of which has a peptide with different conformation. After obtaining .tpr files (at desired temperatures) for each replicas, I loaded them via mdrun, but I got the following error: Fatal error: Nothing to exchange with only one replica --- Why? ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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: RE: [gmx-users] problem with mdrun performing replica exchange MD
Hi Berk, I indicated the number of replicas with -multi option. In additon, I have compiled Gromacs with MPI support. I used the following command line: mdrun -s simul0.tpr -multi 16 -reseed -1 -replex 2500 -Original Message- From: Berk Hess [EMAIL PROTECTED] To: gmx-users@gromacs.org Date: Fri, 23 Nov 2007 10:36:57 +0100 Subject: RE: [gmx-users] problem with mdrun performing replica exchange MD From: OZGE ENGIN [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: gmx-users@gromacs.org Subject: [gmx-users] problem with mdrun performing replica exchange MD Date: Fri, 23 Nov 2007 11:30:53 +0200 Hi All, I am performing replica exchange molecular dynamics simulation(REMD). I have 16 replicas each of which has a peptide with different conformation. After obtaining .tpr files (at desired temperatures) for each replicas, I loaded them via mdrun, but I got the following error: Fatal error: Nothing to exchange with only one replica --- Why? I guess there are two possibilities. Or you did not use the -np option of mdrun to set the number of replicas, or you have not compiled Gromacs with MPI support. Berk. _ Talk with your online friends with Messenger http://www.join.msn.com/messenger/overview ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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 search the archive at http://www.gromacs.org/search before posting! 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: Re: RE: [gmx-users] problem with mdrun performing replica exchange MD
This time, I used the following command line: mpirun -np 8 mdrun_mpi -s simul0_md.tpr -replex 2500 -reseed -1 -multi 8 but I got the following error: Program mdrun_mpi, VERSION 3.3.99_development_20070413 Source code file: gmxfio.c, line: 706 Can not open file: simul00.tpr --- Shit Happens (Pulp Fiction) Error on node 0, will try to stop all the nodes Halting parallel program mdrun_mpi on CPU 0 out of 8 Although I do not have such a file: simul00.tpr -Original Message- From: Berk Hess [EMAIL PROTECTED] To: gmx-users@gromacs.org Date: Fri, 23 Nov 2007 10:58:48 +0100 Subject: Re: RE: [gmx-users] problem with mdrun performing replica exchange MD You need to supply the -np option. In Gromacs 3.3 you don't need to set the -multi option, and -multi does not take an argument. If you use the CVS head branch, you need to set -np and -multi both with an argument. Berk. From: OZGE ENGIN [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: gmx-users@gromacs.org Subject: Re: RE: [gmx-users] problem with mdrun performing replica exchange MD Date: Fri, 23 Nov 2007 11:44:47 +0200 Hi Berk, I indicated the number of replicas with -multi option. In additon, I have compiled Gromacs with MPI support. I used the following command line: mdrun -s simul0.tpr -multi 16 -reseed -1 -replex 2500 -Original Message- From: Berk Hess [EMAIL PROTECTED] To: gmx-users@gromacs.org Date: Fri, 23 Nov 2007 10:36:57 +0100 Subject: RE: [gmx-users] problem with mdrun performing replica exchange MD From: OZGE ENGIN [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: gmx-users@gromacs.org Subject: [gmx-users] problem with mdrun performing replica exchange MD Date: Fri, 23 Nov 2007 11:30:53 +0200 Hi All, I am performing replica exchange molecular dynamics simulation(REMD). I have 16 replicas each of which has a peptide with different conformation. After obtaining .tpr files (at desired temperatures) for each replicas, I loaded them via mdrun, but I got the following error: Fatal error: Nothing to exchange with only one replica --- Why? I guess there are two possibilities. Or you did not use the -np option of mdrun to set the number of replicas, or you have not compiled Gromacs with MPI support. Berk. _ Talk with your online friends with Messenger http://www.join.msn.com/messenger/overview ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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 search the archive at http://www.gromacs.org/search before posting! 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 _ Play online games with your friends with Messenger http://www.join.msn.com/messenger/overview ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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 search the archive at http://www.gromacs.org/search before posting! 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] trjconv does not work
Hi all, I want to extract some frames from the whole trajectory. So, I used -trjconv with (b) and (e) options. P.S: I use the Gromacs 3.3.1 version. But I got the following error: Select a group: 0 Selected 0: 'System' Last frame -1 time0.000 Precision of traj.xtc is 0.001 (nm) WARNING no output, trajectory ended at 10 What is the problem? ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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: Re: [gmx-users] trjconv does not work
The command line ws the following: trjconv -s peptide_b4md.gro -f traj.xtc -b 0.1 -e 0.2 -o file_1.pdb -Original Message- From: Ran Friedman [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Mon, 19 Nov 2007 17:10:51 +0100 Subject: Re: [gmx-users] trjconv does not work Dear Ozge, What was the command line exactly? Ran. OZGE ENGIN wrote: Hi all, I want to extract some frames from the whole trajectory. So, I used -trjconv with (b) and (e) options. P.S: I use the Gromacs 3.3.1 version. But I got the following error: Select a group: 0 Selected 0: 'System' Last frame -1 time0.000 Precision of traj.xtc is 0.001 (nm) WARNING no output, trajectory ended at 10 What is the problem? ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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 search the archive at http://www.gromacs.org/search before posting! 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: Re: [gmx-users] trjconv does not work
The command line was the following: trjconv -s peptide_b4md.gro -f traj.xtc -b 0.1 -e 0.2 -o file_1.pdb -Original Message- From: Ran Friedman [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Mon, 19 Nov 2007 17:10:51 +0100 Subject: Re: [gmx-users] trjconv does not work Dear Ozge, What was the command line exactly? Ran. OZGE ENGIN wrote: Hi all, I want to extract some frames from the whole trajectory. So, I used -trjconv with (b) and (e) options. P.S: I use the Gromacs 3.3.1 version. But I got the following error: Select a group: 0 Selected 0: 'System' Last frame -1 time0.000 Precision of traj.xtc is 0.001 (nm) WARNING no output, trajectory ended at 10 What is the problem? ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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 search the archive at http://www.gromacs.org/search before posting! 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: Re: [gmx-users] trjconv does not work
Of course, I am performing a 40 ns simulation, and 14 ns of it has been finished. What may be the problem? I know, I can extract specific frames via VMD, but it changes atom types after saving in pdb format. -Original Message- From: Ran Friedman [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Mon, 19 Nov 2007 17:53:16 +0100 Subject: Re: [gmx-users] trjconv does not work I see. Do you have any structure between t=0.1ps and t=0.2ps? Ran. OZGE ENGIN wrote: The command line ws the following: trjconv -s peptide_b4md.gro -f traj.xtc -b 0.1 -e 0.2 -o file_1.pdb ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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 search the archive at http://www.gromacs.org/search before posting! 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] (no subject)
I want to use replica exchange method. After obtaining all files at different temperatures, how can I load the e.g 4 separate replica files to the mdrun command? I could not find any information about it. Thank you Oz. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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] Performing simulation at air/water interface
Hi all, I am performing a simulation of peptide at air/water interface. The box vectors are: x,y,z where 2x=2y=z. After loading the trajectory to the vmd, I realized that water molecules moved out of bulk water in the z direction: into the vacuum. However, the peptide also moved out of the bulk water, but at this time, not in the z direction but in the x direction. Although I expanded the box only in the z direction, what may be the probable reason for this? Ozge. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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: Re: [gmx-users] Performing simulation at air/water interface
Thank you for your suggestion, but I have already tried it. -Original Message- From: Pedro Alexandre de Araújo Gomes Lapido Loureiro [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Mon, 5 Nov 2007 16:33:26 -0200 Subject: Re: [gmx-users] Performing simulation at air/water interface Regarding the peptide moving out of the box, it is only a visualization artifact. Try trjconv -pbc inbox. 2007/11/5, OZGE ENGIN [EMAIL PROTECTED]: Hi all, I am performing a simulation of peptide at air/water interface. The box vectors are: x,y,z where 2x=2y=z. After loading the trajectory to the vmd, I realized that water molecules moved out of bulk water in the z direction: into the vacuum. However, the peptide also moved out of the bulk water, but at this time, not in the z direction but in the x direction. Although I expanded the box only in the z direction, what may be the probable reason for this? Ozge. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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 search the archive at http://www.gromacs.org/search before posting! 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] Placing a peptide at the air/water interface
Hi all, I am performing a simulation of an amphilic peptide at air/water interface. I want to start to simulation in which the peptide is placed at the interface. I changed the center of the system so that the center is now located at interface. Then, I used editconf command with -c option in order to center the peptide. I expect to place the peptide at interface. However, instead of placing it at interface, the center of the box is changed its old values. How can I place the peptide at air/water interface before starting a simulation? Thanks in advance Ozge. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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] Placing a peptide at the air/water interface
Hi all, I am performing a simulation of an amphilic peptide at air/water interface. I want to start to simulation in which the peptide is placed at the interface. I changed the center of the system so that the center is now located at interface. Then, I used editconf command with -c option in order to center the peptide. I expect to place the peptide at interface. However, instead of placing it at interface, the center of the box is changed its old values. How can I place the peptide at air/water interface before starting a simulation? Thanks in advance Ozge. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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] Placing a peptide at the air/water interface
Hi Mark, I am so sorry, but I erased your mail before reading it. So, could you please send the mail one more time? It is important to me. Thank you very much Ozge -Original Message- From: OZGE ENGIN [EMAIL PROTECTED] To: gmx-users@gromacs.org Date: Sun, 04 Nov 2007 13:36:02 +0200 Subject: [gmx-users] Placing a peptide at the air/water interface Hi all, I am performing a simulation of an amphilic peptide at air/water interface. I want to start to simulation in which the peptide is placed at the interface. I changed the center of the system so that the center is now located at interface. Then, I used editconf command with -c option in order to center the peptide. I expect to place the peptide at interface. However, instead of placing it at interface, the center of the box is changed its old values. How can I place the peptide at air/water interface before starting a simulation? Thanks in advance Ozge. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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 search the archive at http://www.gromacs.org/search before posting! 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] Addition of ions in vacuum simulations
Hi all, I am simulating a charged peptide in vacuum. I want to neutralize my system by using genion command,and as expected it asks me a continuous solvent group for the replacement; however, I have no solvents. How can I add ions to my system if I am in vacuum? or Is it necessary to add ions while performing simulations in vacuum? Thanks in advance Ozge ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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: Re: [gmx-users] Addition of ions in vacuum simulations
Hi Mark, I think, it is not a chemistry question exactly. Genion command asks for a group whose atoms are replaced with ions. I have no solvent molecules in my system. In this respect, how can I incorporate ions into my system? Thanks Ozge -Original Message- From: Mark Abraham [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Thu, 18 Oct 2007 16:49:15 +1000 (EST) Subject: Re: [gmx-users] Addition of ions in vacuum simulations Hi all, I am simulating a charged peptide in vacuum. I want to neutralize my system by using genion command,and as expected it asks me a continuous solvent group for the replacement; however, I have no solvents. How can I add ions to my system if I am in vacuum? or Is it necessary to add ions while performing simulations in vacuum? This is a chemistry question that will depend on your protein and what you're trying to study. In some cases you might also consider modifying the chemical groups so that there is not an ion there. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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 search the archive at http://www.gromacs.org/search before posting! 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] Tool for visualizing disulphide bonds
Hi all, Is there any tool for the visualization of disulphide bonds along the whole trajectory? Regards, Ozge ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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: Re: [gmx-users] the comm_mode
Hi Yang, I am performing a simulation of a peptide in vacuum, and in the mailing archieve, I read that using of linear option of comm_mode in the vacuum simulations. Is it due to the relatively rapid convergence of molecules in the vacuum environment? Thanks in advance Ozge -Original Message- From: Yang Ye [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Sun, 14 Oct 2007 03:42:12 -0700 (PDT) Subject: Re: [gmx-users] the comm_mode Generally, linear. For simulation in vacumm, you need rotation. With big molecules, equilibration may not be done thoroughly; this may result in very obivious rotation that Linear can not prevent. So visualize your trajectory and check your molecule. If it happens, you need to apply Rotation in the beginning of your simulation for a few ns. Regards, Yang Ye - Original Message From: Dechang Li [EMAIL PROTECTED] To: gmx-users gmx-users@gromacs.org Sent: Sunday, October 14, 2007 5:34:35 PM Subject: [gmx-users] the comm_mode Dear all, There are three options of comm_mode: Linear, Angular and none. The option Angular is said that Remove center of mass translation and rotation around the center of mass. Does it mean the option Angular remove the translation and rotation BOTH ? If I want to do a simulation such as a protein in the explicit water, which option would be better? Or it will be the same? Thank you for your reply. Best regards, 2007-10-14 = Dechang Li, PhD Candidate Department of Engineering Mechanics Tsinghua University Beijing 100084 PR China Tel: +86-10-62773779(O) Email: [EMAIL PROTECTED] = ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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: Re: Re: [gmx-users] the comm_mode
Sorry, but I have to ask some more questions. I have just started to perform simulations in vacuum. I can understand not using of PME in vacuum simulations; however, I can not understand the sentence you wrote : 'rotation is recomended.' COM velocity removal's effect is directly visible. Is it related to conservation of angular momentum? Thank you very much! Oz. -Original Message- From: Yang Ye [EMAIL PROTECTED] To: gmx-users@gromacs.org Date: Sun, 14 Oct 2007 07:07:18 -0700 (PDT) Subject: Re: Re: [gmx-users] the comm_mode - Original Message From: OZGE ENGIN [EMAIL PROTECTED] To: [EMAIL PROTECTED]; gmx-users@gromacs.org Cc: gmx-users@gromacs.org Sent: Sunday, October 14, 2007 8:33:28 PM Subject: Re: Re: [gmx-users] the comm_mode Hi Yang, I am performing a simulation of a peptide in vacuum, and in the mailing archieve, I read that using of linear option of comm_mode in the vacuum simulations. Is it due to the relatively rapid convergence of molecules in the vacuum environment? It is not because of this reason, it is due to PBC. Simulation in vacuum is usually done without PBC, Rotation is recommended. COM velocity removal's effect is directly visible, so if Linear works for you, you may use it. Thanks in advance Ozge -Original Message- From: Yang Ye [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Sun, 14 Oct 2007 03:42:12 -0700 (PDT) Subject: Re: [gmx-users] the comm_mode Generally, linear. For simulation in vacumm, you need rotation. With big molecules, equilibration may not be done thoroughly; this may result in very obivious rotation that Linear can not prevent. So visualize your trajectory and check your molecule. If it happens, you need to apply Rotation in the beginning of your simulation for a few ns. Regards, Yang Ye - Original Message From: Dechang Li [EMAIL PROTECTED] To: gmx-users gmx-users@gromacs.org Sent: Sunday, October 14, 2007 5:34:35 PM Subject: [gmx-users] the comm_mode Dear all, There are three options of comm_mode: Linear, Angular and none. The option Angular is said that Remove center of mass translation and rotation around the center of mass. Does it mean the option Angular remove the translation and rotation BOTH ? If I want to do a simulation such as a protein in the explicit water, which option would be better? Or it will be the same? Thank you for your reply. Best regards, 2007-10-14 = Dechang Li, PhD Candidate Department of Engineering Mechanics Tsinghua University Beijing 100084 PR China Tel: +86-10-62773779(O) Email: [EMAIL PROTECTED] = ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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] Charge of CH2r atoms in Gromos 53A6 force-field
Hi all, I have read the manual of Gromos force field with parameter set 53A6. I am trying to get the topology file of cyclohexane molecule. In a paper which defined the parameters of Gromos 53A5 and 53A6 force-fields, it is said that atoms that are not listed have a zero charge, and the charge of CH2r atoms have not been given in that list. So,to be sure I want to ask again. The charge of CH2r atoms (CH2 groups in a ring) have a zero charge in Gromos 53A6 force-field? thanks Oz. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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] r_list and r_coulomb values while using PME
Hi all, I can not understand why it is required to take same values for both r_list and r_coulomb parameters when using PME for calculation of electrostatic interactions? I read archieve, and gromacs manual. In archieve, similar question had been posted, but not replied yet. Thanks in advance Oz. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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: Re: [gmx-users] r_list and r_coulomb values while using PME
'The force is not the derivative of the potential', is it due to the types of calculations performed in PME, using of FFT for reciprocal sum? Because it does not matter while using reaction-field method. Sorry, this phenomenon is a little complicated to me :) Thanks for your attention! Oz. -Original Message- From: David van der Spoel [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Sat, 01 Sep 2007 13:37:05 +0200 Subject: Re: [gmx-users] r_list and r_coulomb values while using PME OZGE ENGIN wrote: Hi all, I can not understand why it is required to take same values for both r_list and r_coulomb parameters when using PME for calculation of electrostatic interactions? I read archieve, and gromacs manual. In archieve, similar question had been posted, but not replied yet. Thanks in advance if rlist rcoulomb you will have a twin range interaction, meaning the atom pair interactions for distance between these two will be computed every nstlist steps only, while the interaction beyond rcoulomb will be computed at each time step. this will lead to bad energy conservation, since the force is not the derivative of the potential. Oz. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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 -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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 search the archive at http://www.gromacs.org/search before posting! 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: Re: [gmx-users] r_list and r_coulomb values while using PME
So, using twin-range cut-off does not violate the energy conservation for RC method, but it violates for PME method. Is this the case ? -Original Message- From: David van der Spoel [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Sat, 01 Sep 2007 14:48:03 +0200 Subject: Re: [gmx-users] r_list and r_coulomb values while using PME OZGE ENGIN wrote: 'The force is not the derivative of the potential', is it due to the types of calculations performed in PME, using of FFT for reciprocal sum? Because it does not matter while using reaction-field method. Sorry, this phenomenon is a little complicated to me :) this is only when you combine twin range (rcoulomb rlist) and PME. then the forces for a certain distance range are not computed at each time step while the others are. you may want to (re)read the PME papers and/or the gromacs manual about twin range. Thanks for your attention! Oz. -Original Message- From: David van der Spoel [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Sat, 01 Sep 2007 13:37:05 +0200 Subject: Re: [gmx-users] r_list and r_coulomb values while using PME OZGE ENGIN wrote: Hi all, I can not understand why it is required to take same values for both r_list and r_coulomb parameters when using PME for calculation of electrostatic interactions? I read archieve, and gromacs manual. In archieve, similar question had been posted, but not replied yet. Thanks in advance if rlist rcoulomb you will have a twin range interaction, meaning the atom pair interactions for distance between these two will be computed every nstlist steps only, while the interaction beyond rcoulomb will be computed at each time step. this will lead to bad energy conservation, since the force is not the derivative of the potential. Oz. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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 -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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 search the archive at http://www.gromacs.org/search before posting! 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] Appropriate command for measuring density of the whole simulation box along the trajectory
Hi all, I want to measure the density or volume of the whole simulation box not only the molecule. I could not find an appropriate command. I found some;however, they measured the partial densities across the box. Thanks in advance... Ozge ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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] Minimization of a box of capped tryptophan (trp)
Hi all, As you suggest David I used genconf command without -rot option. I minimized a single capped trp molecule and got the minimized molecule and used that molecule with genconf command in order to create a box. Then, I solvated capped trp molecule within the created box with genbox command. I wanted the box to have a total of 200 capped trp molecules. In this respect, I used -maxsol 200 option. However, the resultant system had only 11 capped trp molecules. What may be the problem? Thanks Oz. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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] Unusual structures generated by GENCONF command and resultant minimization problem
Hi gromacs-users, I want to simulate a box of that is composed of capped (ACE and NME to N and C termini, respectively) tryptophan molecules. As a first stage, I minimized single capped trp molecule, and then used it with genconf command along with the options -rot ans -nbox. In this case, I changed the gro file of capped trp molecule such that it was treated as a single molecule rather than three (cappes and the trp molecule itself). (It was necessary to be able to use that molecule with genconf command.) After that, I could obtain a box of trp molecules. However, when I looked at it by using VMD, I saw that some of them had unusual bonds. So it caused not to minimization of my system. The steepest descent minimization was terminated before the desired criterion was reached. Although I used a minimized capped trp molecule with genconf command, the resultant box contained some trp molecules that have unusual structures. How can I overcome that problem? Thanks in advance... Oz. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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] Problem with g_rdf /option com
Hi, I want to get the radial distribution of my system which is composed of a box of capped alanine residues (CAR). In this respect, I used g_rdf command with -com option. I chose one of the CAR s as the first, and the others as the second group. In manual, for -com option, it is written that the center of mass is chosen only for the first group. Does it mean that for the second group all the atoms are taken into consideration? If so, is there any option for taking the center of masses of molecules in the second group? Thanks Ozge. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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: Re: [gmx-users] adding counter ions
Dear Mark, I had read papers about the simulations of charged systems. You' re right. In these studies, the distance between the charged residues have been controlled during the simulation. In this respect, you suggest me not adding counter ions to the system: Providing the distance between the oppositely charged residues :-) is not far apart than the optimum which means that they are located at such a distance that they have the ability to cancel each other. Thank you... Ozge Engin -Original Message- From: Mark Abraham [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Tue, 12 Jun 2007 10:49:54 +1000 Subject: Re: [gmx-users] adding counter ions OZGE ENGIN wrote: Hi all, My peptide contains two adversely charged residues. I use PME option for the investigation of electrostatic interactions within my system. The total charge of the box must be neutral. Since the system contains adversely charged residues, is it still necessary to add counter ions into the system? adversely charged doesn't mean the same thing as oppositely charged :-) While overall periodic cell neutrality has been achieved here, you will still have separated charges that will attract each other, potentially distorting your equilibrium state. In a real system, each of these residues would likely have a counter-ion present closer than the other residue - but of course you know how far apart these residues are, don't you? Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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 search the archive at http://www.gromacs.org/search before posting! 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] adding counter ions
Hi all, My peptide contains two adversely charged residues. I use PME option for the investigation of electrostatic interactions within my system. The total charge of the box must be neutral. Since the system contains adversely charged residues, is it still necessary to add counter ions into the system? Thanks in advance! Ozge Engin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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] problem with the output file of g_density
Dear gromacs-users, I have a problem with the output file of g_density. It uses .tpr and .trr files in order to make calculations. I have made the .trr file using the parameters below. Since total step size is 100 and I have written the coordinates at each 50 steps, I expect to have more than 50 values in the output file of g_density; but there are only 50. Why is this the case? Thank in advance ... Ozge dt = 0.002;ps nsteps = 100 nstcomm = 1 nstxout = 50 nstvout = 0 nstfout = 0 nstlist = 10 ns_type = grid ; Output frequency for energies to log file and energy file = nstlog = 50 nstenergy = 50 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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] problem with position-restrained dynamics of a charged system
Hi all, I have a problem with position-restrained (pr) dynamics of a charged residue in a water box. Up to the position-restrained step, the method worked well; however, it gave the following error in the pr step: Fatal error: number of coordinates in coordinate file (lysine_b4pr.gro, 767) does not match topology (lysine.top, 0) I could not understand the error because the lysine.top file has already contained the appropriate numbers of atoms defined for protein, ion, and solvent molecules. Moreover, I used the same topology file in the preceding step and it worked. So, what may be the problem? Thanks in advance! Ozge Engin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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: Re: [gmx-users] problem with position-restrained dynamics of a charged system
Yes, Sebastien! It ends as you wrote. So, it contains info about the number of atoms, and it worked for the previous step. I could not understand the problem :( -Original Message- From: sebastien santini [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Tue, 22 May 2007 14:27:18 +0100 Subject: Re: [gmx-users] problem with position-restrained dynamics of a charged system It seems your topology does not contain any information about number of atoms etc ... Does your file end with lines like this (for example): ... [ molecules ] ; Compound #mol Protein 1 NA+ 12 SOL 1589 OZGE ENGIN a écrit : Hi all, I have a problem with position-restrained (pr) dynamics of a charged residue in a water box. Up to the position-restrained step, the method worked well; however, it gave the following error in the pr step: Fatal error: number of coordinates in coordinate file (lysine_b4pr.gro, 767) does not match topology (lysine.top, 0) I could not understand the error because the lysine.top file has already contained the appropriate numbers of atoms defined for protein, ion, and solvent molecules. Moreover, I used the same topology file in the preceding step and it worked. So, what may be the problem? Thanks in advance! Ozge Engin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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 -- ___ Sébastien SANTINI, PhD http://sebastien.santini.free.fr CBMN, Faculté Universitaire des Sciences Agronomiques Passage des déportés, 2 B-5030 Gembloux, BELGIQUE GSM: 00 32 (0)4 98 59 53 65 ___ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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 search the archive at http://www.gromacs.org/search before posting! 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: Re: [gmx-users] problem with position-restrained dynamics of a charged system
Yes, Sebastien! It ends as you wrote. So, it contains info about the numbers of atoms, and it worked for the previous step. I could not understand the problem :( -Original Message- From: sebastien santini [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Tue, 22 May 2007 14:27:18 +0100 Subject: Re: [gmx-users] problem with position-restrained dynamics of a charged system It seems your topology does not contain any information about number of atoms etc ... Does your file end with lines like this (for example): ... [ molecules ] ; Compound #mol Protein 1 NA+ 12 SOL 1589 OZGE ENGIN a écrit : Hi all, I have a problem with position-restrained (pr) dynamics of a charged residue in a water box. Up to the position-restrained step, the method worked well; however, it gave the following error in the pr step: Fatal error: number of coordinates in coordinate file (lysine_b4pr.gro, 767) does not match topology (lysine.top, 0) I could not understand the error because the lysine.top file has already contained the appropriate numbers of atoms defined for protein, ion, and solvent molecules. Moreover, I used the same topology file in the preceding step and it worked. So, what may be the problem? Thanks in advance! Ozge Engin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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 -- ___ Sébastien SANTINI, PhD http://sebastien.santini.free.fr CBMN, Faculté Universitaire des Sciences Agronomiques Passage des déportés, 2 B-5030 Gembloux, BELGIQUE GSM: 00 32 (0)4 98 59 53 65 ___ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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 search the archive at http://www.gromacs.org/search before posting! 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: Re: [gmx-users] problem with position-restrained dynamics of a charged system
Thank you very much for your attention :) I attached the needed gro and top files. -Original Message- From: sebastien santini [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Tue, 22 May 2007 14:52:13 +0100 Subject: Re: [gmx-users] problem with position-restrained dynamics of a charged system Maybe you have forget to include something (I don't know exactly what) ... is it possible to post your top and gro files (attached and zipped) ? it will be easier to find what happened :P . OZGE ENGIN a écrit : Yes, Sebastien! It ends as you wrote. So, it contains info about the number of atoms, and it worked for the previous step. I could not understand the problem :( -Original Message- From: sebastien santini [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Tue, 22 May 2007 14:27:18 +0100 Subject: Re: [gmx-users] problem with position-restrained dynamics of a charged system It seems your topology does not contain any information about number of atoms etc ... Does your file end with lines like this (for example): ... [ molecules ] ; Compound #mol Protein 1 NA+ 12 SOL 1589 OZGE ENGIN a écrit : Hi all, I have a problem with position-restrained (pr) dynamics of a charged residue in a water box. Up to the position-restrained step, the method worked well; however, it gave the following error in the pr step: Fatal error: number of coordinates in coordinate file (lysine_b4pr.gro, 767) does not match topology (lysine.top, 0) I could not understand the error because the lysine.top file has already contained the appropriate numbers of atoms defined for protein, ion, and solvent molecules. Moreover, I used the same topology file in the preceding step and it worked. So, what may be the problem? Thanks in advance! Ozge Engin -- ___ Sébastien SANTINI, PhD http://sebastien.santini.free.fr CBMN, Faculté Universitaire des Sciences Agronomiques Passage des déportés, 2 B-5030 Gembloux, BELGIQUE GSM: 00 32 (0)4 98 59 53 65 ___ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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 files.rar Description: Binary data ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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: Re: [gmx-users] problem with position-restrained dynamics of a charged system
Thank you very much for your attention :) I attached the needed gro and top files. -Original Message- From: sebastien santini [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Tue, 22 May 2007 14:52:13 +0100 Subject: Re: [gmx-users] problem with position-restrained dynamics of a charged system Maybe you have forget to include something (I don't know exactly what) ... is it possible to post your top and gro files (attached and zipped) ? it will be easier to find what happened :P . OZGE ENGIN a écrit : Yes, Sebastien! It ends as you wrote. So, it contains info about the number of atoms, and it worked for the previous step. I could not understand the problem :( -Original Message- From: sebastien santini [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Tue, 22 May 2007 14:27:18 +0100 Subject: Re: [gmx-users] problem with position-restrained dynamics of a charged system It seems your topology does not contain any information about number of atoms etc ... Does your file end with lines like this (for example): ... [ molecules ] ; Compound #mol Protein 1 NA+ 12 SOL 1589 OZGE ENGIN a écrit : Hi all, I have a problem with position-restrained (pr) dynamics of a charged residue in a water box. Up to the position-restrained step, the method worked well; however, it gave the following error in the pr step: Fatal error: number of coordinates in coordinate file (lysine_b4pr.gro, 767) does not match topology (lysine.top, 0) I could not understand the error because the lysine.top file has already contained the appropriate numbers of atoms defined for protein, ion, and solvent molecules. Moreover, I used the same topology file in the preceding step and it worked. So, what may be the problem? Thanks in advance! Ozge Engin -- ___ Sébastien SANTINI, PhD http://sebastien.santini.free.fr CBMN, Faculté Universitaire des Sciences Agronomiques Passage des déportés, 2 B-5030 Gembloux, BELGIQUE GSM: 00 32 (0)4 98 59 53 65 ___ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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 files.rar Description: Binary data ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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] problem with genion
Hi gromacs-users, I have a problem with the simulation of a capped lysine residue.I followed the tutorial step by step. I added 1 Cl ion into my system in order to neutralize the overall charge by using genion, and then used the grompp command and I encountered with the following error: Program grompp, VERSION 3.3.1 Source code file: toppush.c, line: 891 Fatal error: moleculetype CU1+ is redefined What is the problem? Thanks in advance Ozge Engin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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] (no subject)
Hi, First of all, I wish, everything is o.k for everybody :) I have a question about the g_rdf command. I read the mailing list but I could not find any problem simiIar to mine. I want to calculate the radial distribution function of my system which consists of tripeptide and water molecules. In this respect, I select two groups: the peptide as the first and the water molecules as the second.Then I plotted the given rdf.xvg file, and what I saw was not an expected one. The distribution of particles increased with respect to increasing distance. I could not get the values of g(r ) on the y axis.The distribution did not show the first and the second peaks that correspond to the first and the second hydration shells, respectively. What is the problem? Thanks in advance Ozge Engin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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] problem with g_rdf
Hi, First of all, I wish, everything is o.k for everybody :) I have a question about the g_rdf command. I read the mailing list but I could not find any problem simiIar to mine. I want to calculate the radial distribution function of my system which consists of tripeptide and water molecules. In this respect, I select two groups: the peptide as the first and the water molecules as the second.Then I plotted the given rdf.xvg file, and what I saw was not an expected one. The distribution of particles increased with respect to increasing distance. I could not get the values of g(r ) on the y axis.The distribution did not show the first and the second peaks that correspond to the first and the second hydration shells, respectively. What is the problem? Thanks in advance Ozge Engin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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] Appropriate tool to get the number of solventmolecules within a cutoff distance around protein molecule
Thank you very much Anthony,I will try it!
Ozge
- Original Message -
From: Anthony Cruz Balberdi [EMAIL PROTECTED]
To: [EMAIL PROTECTED]
Cc: gmx-users@gromacs.org
Sent: Monday, March 19, 2007 3:19 PM
Subject: Re: [gmx-users] Appropriate tool to get the number of
solventmolecules within a cutoff distance around protein molecule
Hi Ozge:
You can use a script in VMD to do the work. In VMD you could make various
atom selection and use it in the script. You
could use something like this:
set outfile [open sol_within_prot.dat w];
set nf [molinfo top get numframes]
set frame0 [atomselect top protein frame 0]
# water calculation loop
for {set i 1 } {$i $nf } { incr i } {
set prot [atomselect top protein frame $i]
$prot move [measure fit $prot $frame0]
set sol2keep [atomselect top (same residue as (within 2 of protein))
and resname SOL frame $i]
set nummolP [$sol2keep num]
set nummolR [expr $nummolP/3]
puts $outfile $frame $nummolR
puts $frame
}
close $outfile
Probably you will need to fit your trajectory if your protein go near the
edge of the box
because VMD does not take in account the PBC in this type of calculation.
Anthony
OZGE ENGIN [EMAIL PROTECTED] wrote:
Hi,
I want to calculate the number of solvent molecules within a cutoff distance
around the protein molecule. I could not
find the appropriate command for this in manual. Moreover, I could not
understand the information for g_sorient.Could
you give me a more detailed explanation for this?
Thanks in advance
Ozge Engin
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-
Antes ahora y siempre COLEGIO
University of Puerto Rico at Mayaguez
http://www.uprm.edu
-
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[gmx-users] Appropriate tool to get the number of solvent molecules within a cutoff distance around protein molecule
Hi, I want to calculate the number of solvent molecules within a cutoff distance around the protein molecule. I could not find the appropriate command for this in manual. Moreover, I could not understand the information for g_sorient.Could you give me a more detailed explanation for this? Thanks in advance Ozge Engin ___ 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: Re: [gmx-users] Appropriate tool to get the number of solvent molecules within a cutoff distance around protein molecule
Thank you very much for your attention! Best regards, Ozge Engin -Original Message- From: Yang Ye [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Sun, 18 Mar 2007 00:35:13 +0800 Subject: Re: [gmx-users] Appropriate tool to get the number of solvent molecules within a cutoff distance around protein molecule try g_trjorder. Some code modification may be needed. Regards, Yang Ye OZGE ENGIN wrote: Hi, I want to calculate the number of solvent molecules within a cutoff distance around the protein molecule. I could not find the appropriate command for this in manual. Moreover, I could not understand the information for g_sorient.Could you give me a more detailed explanation for this? Thanks in advance Ozge Engin ___ 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 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] Appropriate tool to get the number of solvent molecules within a cutoff distance around protein molecule
Hi, I want to calculate the number of solvent molecules within a cutoff distance around the protein molecule. I could not find the appropriate command for this in manual. Moreover, I could not understand the information for g_sorient.Could you give me a more detailed explanation for this? Thanks in advance Ozge Engin ___ 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] g_mindist
Hi, I forgot to ask my other question :) When I use the g_mindist command, it asks me to select two groups for which the distance will be calculated. I am confused for the following: I want to calculate the minimum distance among three side chains of my molecule in all combinations. So, if I choose the side chain (system 8) option for this command twice, which side chains will be taken into consideration? Thanks in advance Ozge Engin ___ 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] problem with trjconv
Hi, I have a problem with the trjconv command. I performed a 30 ns simulation, and wanted to analyze hydrogen bonds formed between protein and water molecules. In this respect, I converted the xtc file into a pdb file by selecting system option. As you can understand the overall file was such a large file that I could not handle it. So, I want to know whether there is any possibility to select water molecules within a cutoff value or to extract frames within given time steps? For instance, at every 70 th step, from 70 ps to 80 ps. Thanks in advance Ozge ___ 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: Re: [gmx-users] problem with trjconv
Hi, First of all, thank you for your attention. I used g_hbond in order to analyze hydrogen bonds formed;but, I need a more detailed information. The command that you mentioned is capable of giving information about hydrogen bonds formed in each frame. However, I want to investigate the exact donor and acceptor groups in each frame. In this respect, I converted the xtc file to a pdb file to get all of the coordinates of both water and protein molecules. What should I do? Thanks in advance Ozge -Original Message- From: Tsjerk Wassenaar [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Wed, 28 Feb 2007 17:52:34 +0100 Subject: Re: [gmx-users] problem with trjconv Hi Ozge, Why do you first want to go to a .pdb trajectory? Gromacs comes with g_hbond, which can analyze hydrogen bonds for you, as well as giving you an index file containing the atoms involved in hydrogen bonds, which you can use to extract those from your trajectory. In addition, g_hbond also does normal contacts, other than hydrogen bonds. Tsjerk On 2/28/07, Mark Abraham [EMAIL PROTECTED] wrote: OZGE ENGIN wrote: Hi, I have a problem with the trjconv command. I performed a 30 ns simulation, and wanted to analyze hydrogen bonds formed between protein and water molecules. In this respect, I converted the xtc file into a pdb file by selecting system option. As you can understand the overall file was such a large file that I could not handle it. So, I want to know whether there is any possibility to select water molecules within a cutoff value or to extract frames within given time steps? For instance, at every 70 th step, from 70 ps to 80 ps. If you read the man page for trjconv, you will see an option to do the latter. I don't think the former is implemented in the gromacs utilities. 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 -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ 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] Comparison of hydrogen bond number
Hi, I could not understand a point related to the calculation of hydrogen bond numbers. In order to be sure, I wrote a script in which the hydrogen bond numbers were calculated during the whole trajectory. Firstly, I used the 30.0 degrees and 0.35 nm criteria, and I compared the results of two: The numbers were the same. After that, I tried the 60.0 and 0.35 nm criteria, but this time, the numbers were not the same. What is the problem? I am so confused. Thanks in advance Özge ENGİN Department of Computational Science and Engineering Koc University, Istanbul ___ 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] trjconv(extraction of certain frames)
Hi, I have a question about the trjconv command. I simulated my system for 30 ns, and got 30 frames. Now, I want to extract some frames from that whole: beginning at every 70 th ps lengthing to the 80 th ps, and to write them in a pdf file. Thanks in advance! Özge Engin Department of Computational Science and Engineering Koc University ___ 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] hbhelix,hbond,hbnum files
Hi, I have the following problem: My system consists of a capped three-alanine residues embedded in a box with 750 water molecules. I want to analyze the hydrogen bonds formed in each frame. In this respect, I used the -hx option to investigate the exact contributors of the hbonds in each frame since its columns give the corresponding residue pairs of the hbonds. At the same time, I used the -hbn option, and got the corresponding index file. In the hbhelix.xvg file, the n-n+2,n-n+3, and the n-n+4 columns were empty although the hbond.ndx file indicated that there were hbonds between the n-n+2,n-n+3,and the n-n+4 residue pairs, so I understood that the caps were not taken into account when calculating the hbonds for the helix. Relying on such differences, I expected to see some differences between these two files (hbhelix.xvg and hbnum.xvg), but this was not the case, they were the same. The hbonds between the mentioned residue pairs above were not included in the hbnum.xvg file although they were included in the hbond.xvg file. Why is this the case? Why are there any differences? Thanks in advance! ozge ___ 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
