[gmx-users] Failed to lock: md.log. No locks available.
Hi, Failed to lock: md.log. No locks available. still the same problem I met before, once I terminated, resume not work, there is a md.log file. $ mount /dev/sda1 on / type ext3 (rw) none on /proc type proc (rw) none on /sys type sysfs (rw) none on /dev/pts type devpts (rw,gid=5,mode=620) usbfs on /proc/bus/usb type usbfs (rw) none on /dev/shm type tmpfs (rw) none on /proc/sys/fs/binfmt_misc type binfmt_misc (rw) sunrpc on /var/lib/nfs/rpc_pipefs type rpc_pipefs (rw) honeydewlocal:/vol/hpc_vol/HomeHPC on /home type nfs (rw,rsize=32k,wsize=32k,intr,hard,tcp,addr=192.168.5.83) The /home is mounting on the last one. CPU: 8 Intel(R) Xeon(R) Dual-Core 3.33 Ghz Memory: 114GB RAM HDD Size: 744GB OS: CentOS 4 (64-bits) Thanks for any suggestions, any additional info you need please let me know, Best regards, -- 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
Re: [gmx-users] System blows up
Dear List and Mark I followed your suggestions equilibrating the proteins of my complex separately. In both cases i'm able to correctly equilibrate the system and to perform a short md of 500ps. So I suppose that when i simulate both protein together somewhere there is a clash. Now how could I highlight the problem? In your opinion the clash could be more probably due to solvent molecules or to my proteins perhaps too near each other? Thank you very much Guido 2012/1/11 Mark Abraham mark.abra...@anu.edu.au On 11/01/2012 8:35 PM, Guido Leoni wrote: Dear List I'm newbie to gromacs (sigh). I'm simulating the interaction between two proteins(chrystallographic structures) following the spider toxin tutorial. I'm able to correctly minimize ( E1000) and equilibrate (400 ps ) the system. No error message appears to me and I'm quite sure that my starting structures have no steric clashes. My .mdp files are equal to the tutorial description excepted for the choosen timesteps (400 ps in equilibration and 1000 ps in dynamics). When I run the dynamic (launching gromacs with mpi) I retrieve after 7 ps the following error message 2 particles communicated to PME node 3 are more than a cell length out of the domain decomposition cell of their charge group I suppose that this is due to the energy of some components that blow up. Please how can i check which components are responsible for the problem? I'm also looking the instruction on the web site but they appear to me a bit cryptic. For example If the crash is happening relatively early (within a few steps), set nstxout (or nstxtcout) to 1, capturing all possible frames. Watch the resulting trajectory to see which atoms/residues/molecules become unstable first. I looked the resulting trajectories of the 2 proteins with ngmx but they seem to be always in the box and it is impossible to graphically check the water molecules . The next piece of advice is to simplify your problem. If you can get each of your proteins to equilibrate on their own, then you probably have an atomic clash after all. If one doesn't equilibrate, then maybe your simulation conditions or topology is suspect. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Guido Leoni National Research Institute on Food and Nutrition (I.N.R.A.N.) via Ardeatina 546 00178 Rome Italy tel + 39 06 51 49 41 (operator) + 39 06 51 49 4498 (direct) -- 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] beads in martini corse-grained
Dear Prof. I don't know about definition of sulfuric acid in Martini Corse-Grained, May I ask you to help me, Please? And Please say me about my definition of aniline as SC4, SC4, SNd that is correct? Best Regards Sara -- 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
Re: [gmx-users] Failed to lock: md.log. No locks available.
On 13/01/2012 7:08 PM, lina wrote: Hi, Failed to lock: md.log. No locks available. mdrun locks various files at various points. If it can't then GROMACS won't continue, but the problem lies with the file system, and not with GROMACS. Possibly some phantom process still thinks it owns the file. Mark still the same problem I met before, once I terminated, resume not work, there is a md.log file. $ mount /dev/sda1 on / type ext3 (rw) none on /proc type proc (rw) none on /sys type sysfs (rw) none on /dev/pts type devpts (rw,gid=5,mode=620) usbfs on /proc/bus/usb type usbfs (rw) none on /dev/shm type tmpfs (rw) none on /proc/sys/fs/binfmt_misc type binfmt_misc (rw) sunrpc on /var/lib/nfs/rpc_pipefs type rpc_pipefs (rw) honeydewlocal:/vol/hpc_vol/HomeHPC on /home type nfs (rw,rsize=32k,wsize=32k,intr,hard,tcp,addr=192.168.5.83) The /home is mounting on the last one. CPU: 8 Intel(R) Xeon(R) Dual-Core 3.33 Ghz Memory: 114GB RAM HDD Size: 744GB OS: CentOS 4 (64-bits) Thanks for any suggestions, any additional info you need please let me know, Best regards, -- 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] (no subject)
Hi all, I am new to the Gromacs and just started to use Gromacs for MD simulations. I am tring to extend the simulation (protein in a box) 10 ns more. For this, I used the following command: grompp -f md.mdp -c md_first.gro -t md_first.cpt -p topol.top -o md_second.tpr mdrun It seems to run.. I am just wondering am I right or should I also use the tpbconv as it is stated in the http://www.gromacs.org/Documentation/How-tos/Extending_Simulations. Thanks, Turgay -- 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
Re: [gmx-users] Failed to lock: md.log. No locks available.
On Fri, Jan 13, 2012 at 4:57 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 13/01/2012 7:08 PM, lina wrote: Hi, Failed to lock: md.log. No locks available. mdrun locks various files at various points. If it can't then GROMACS won't continue, but the problem lies with the file system, and not with GROMACS. Possibly some phantom process still thinks it owns the file. It's something relevant to the server. I am not experienced to figure it out even did some rough try. will drop an email to administrator. Thanks, Mark still the same problem I met before, once I terminated, resume not work, there is a md.log file. $ mount /dev/sda1 on / type ext3 (rw) none on /proc type proc (rw) none on /sys type sysfs (rw) none on /dev/pts type devpts (rw,gid=5,mode=620) usbfs on /proc/bus/usb type usbfs (rw) none on /dev/shm type tmpfs (rw) none on /proc/sys/fs/binfmt_misc type binfmt_misc (rw) sunrpc on /var/lib/nfs/rpc_pipefs type rpc_pipefs (rw) honeydewlocal:/vol/hpc_vol/HomeHPC on /home type nfs (rw,rsize=32k,wsize=32k,intr,hard,tcp,addr=192.168.5.83) The /home is mounting on the last one. CPU: 8 Intel(R) Xeon(R) Dual-Core 3.33 Ghz Memory: 114GB RAM HDD Size: 744GB OS: CentOS 4 (64-bits) Thanks for any suggestions, any additional info you need please let me know, Best regards, -- 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/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 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
Re: [gmx-users] Failed to lock: md.log. No locks available.
There is a solution in this mailing list sometime before: mv md.log to some other folder and copy it back. Jianguo From: lina lina.lastn...@gmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Friday, 13 January 2012, 18:51 Subject: Re: [gmx-users] Failed to lock: md.log. No locks available. On Fri, Jan 13, 2012 at 4:57 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 13/01/2012 7:08 PM, lina wrote: Hi, Failed to lock: md.log. No locks available. mdrun locks various files at various points. If it can't then GROMACS won't continue, but the problem lies with the file system, and not with GROMACS. Possibly some phantom process still thinks it owns the file. It's something relevant to the server. I am not experienced to figure it out even did some rough try. will drop an email to administrator. Thanks, Mark still the same problem I met before, once I terminated, resume not work, there is a md.log file. $ mount /dev/sda1 on / type ext3 (rw) none on /proc type proc (rw) none on /sys type sysfs (rw) none on /dev/pts type devpts (rw,gid=5,mode=620) usbfs on /proc/bus/usb type usbfs (rw) none on /dev/shm type tmpfs (rw) none on /proc/sys/fs/binfmt_misc type binfmt_misc (rw) sunrpc on /var/lib/nfs/rpc_pipefs type rpc_pipefs (rw) honeydewlocal:/vol/hpc_vol/HomeHPC on /home type nfs (rw,rsize=32k,wsize=32k,intr,hard,tcp,addr=192.168.5.83) The /home is mounting on the last one. CPU: 8 Intel(R) Xeon(R) Dual-Core 3.33 Ghz Memory: 114GB RAM HDD Size: 744GB OS: CentOS 4 (64-bits) Thanks for any suggestions, any additional info you need please let me know, Best regards, -- 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/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 mailing list gmx-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 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] Constructing covalent bond between protein-ligand complex
Dear all, Guided by gmxusers' list I have used gmx_top_tools.tgz (http://www.gromacs.org/Downloads/User_contributions/Other_software) to prepare the protein-ligand complex linked by a covalent bond. Unfortunately the tool renumtop is detecting a duplicate atom but not updating its number. Only gives an error message: ; ERROR: duplicate atom label '4968' for atom #4968 (already used for atom #4968) I used the command ./renumtop topol_Protein_chain_A.itp topol_Chain_B.itp. may be I am doing something wrong. Please help. Suman Nandy Suman Kumar Nandy Senior Research Fellow Department of Biochemistry Biophysics University of Kalyani Kalyani-741235 India.-- 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
Re: [gmx-users] Failed to lock: md.log. No locks available.
On Fri, Jan 13, 2012 at 7:04 PM, Jianguo Li ljg...@yahoo.com.sg wrote: There is a solution in this mailing list sometime before: mv md.log to some other folder and copy it back. Jianguo I tried, not work. Thanks, From: lina lina.lastn...@gmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Friday, 13 January 2012, 18:51 Subject: Re: [gmx-users] Failed to lock: md.log. No locks available. On Fri, Jan 13, 2012 at 4:57 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 13/01/2012 7:08 PM, lina wrote: Hi, Failed to lock: md.log. No locks available. mdrun locks various files at various points. If it can't then GROMACS won't continue, but the problem lies with the file system, and not with GROMACS. Possibly some phantom process still thinks it owns the file. It's something relevant to the server. I am not experienced to figure it out even did some rough try. will drop an email to administrator. Thanks, Mark still the same problem I met before, once I terminated, resume not work, there is a md.log file. $ mount /dev/sda1 on / type ext3 (rw) none on /proc type proc (rw) none on /sys type sysfs (rw) none on /dev/pts type devpts (rw,gid=5,mode=620) usbfs on /proc/bus/usb type usbfs (rw) none on /dev/shm type tmpfs (rw) none on /proc/sys/fs/binfmt_misc type binfmt_misc (rw) sunrpc on /var/lib/nfs/rpc_pipefs type rpc_pipefs (rw) honeydewlocal:/vol/hpc_vol/HomeHPC on /home type nfs (rw,rsize=32k,wsize=32k,intr,hard,tcp,addr=192.168.5.83) The /home is mounting on the last one. CPU: 8 Intel(R) Xeon(R) Dual-Core 3.33 Ghz Memory: 114GB RAM HDD Size: 744GB OS: CentOS 4 (64-bits) Thanks for any suggestions, any additional info you need please let me know, Best regards, -- 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/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 mailing list gmx-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 mailing list gmx-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 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] 1-4 Scaling problem of ASN-NAG from GLYCAM
Dear All, The protein on which I am working, have few ASN residues which are N-linked with the N-acetyl-glucosamine (NAG). I have taken the parameters of the NAG and N-linked ASN from the GLYCAM_06. I have added this N-linked ASN as a new residue in aminoacids.rtp file and accordingly all the parametrs are added in respective files. After this both pdb2gmx and grompp are working without any error. But the problem I am facing is related to 1-4 scaling. For the GLYCAM, fudgeLJ and fudgeQQ should be 1. I have read the following mailing post that how one can mix the fudgeLJ and fudgeQQ in GROMACS. http://lists.gromacs.org/pipermail/gmx-users/2011-April/060839.html In the manual, I have come across with two type of pairs function. In function type 1, two parameters are needed and is used as default. But, in function type 2, five parameters are needed: fudgeQQ, q_i, q_j, V(cr) and W(cr). So can I replace function type 1 with 2 in the pdb2gmx generated topology for only those pairs belong to the NAG and side chains of N-linked ASN. So that, I can use fudgeQQ of 1.0, q_i / q_j from the rtp/topology and V(cr) / W(cr) (calculated from the sigma and epsilon using combination rule) for those pairs. Will this give No Scaling for 1-4 pair belong to NAG and side chains of N-linked ASN. Or another which I found “those 1-4 pairs belong to side chains of N-linked ASN and NAG, so I could remove them from [ pairs ] section and put into the [ pairs_nb ] section.” Then these pairs will be treated as normal non-bonded pairs. Please suggest me, what I can do in this regard and which is the correct way. Thank you in advance. -- With Regards, Rashmi Kumari Research Scholar School of Computational and Integrative Sciences Jawaharlal Nehru University New Delhi- 110067. -- 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] pdb2gmx -ss option
Dear all, I'm using the old 3.3.3 version of gromacs and I try to use the -ss option of pdb2gmx to select interactively the ss bridge in my protein. But I don't remark any change between using -ss option and not using it. The -inter option give me some interactive options such as lys or arg but not ss interactive selection. Could you help me? Thanks -- Pierre THEVENET -- 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] Coarse-graining and cut-offs
Dear all, first of all, sorry to this rather conceptional question, which is not totally to GROMOACS related. But probably anyone of you can help. In my simulations I use mesitylene as a solvent. In future i want to coarse-grain the full atomic mesitylene to an effective one-particle. For this i did a NPT-simulation to obtain the RDF (with regard to the COM of the molecules) from which i want to calculate an effective interaction potential by iterative boltzmann. The full-atomistic simulations (slovate + solvent) employed a cut-off of 1.4 nm. At this distance (1.4 nm) the RDF shows it second minimum (RDF=0.97) and after 1.8 nm the RDF is around 1.0 +/- 0.15 (I got the RDF only up to a distance of 2.3 nm). Now my question is how long should be the table for the effective potential (i.e. maximum distance for an interaction)? If i would use 1.4 nm, i would have a jump in the interaction potential (which is normal due to the truncation of the cut-off). But for coulomb-interaction one would have PME or other stuff which would correct the artifects to some degree. Or would it be better to use a long interaction table (interactions at longer distances) and truncate the table at a distance after 1.4 nm where the RDF is equal to 1? Hope anybody can give some insight. Greetings Thomas -- 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] Umbrella Sampling application
Dear Gmx Users! I do protein-ligand simulations and I am interested in binding free energy. My ligand is not charged molecule, there is no specific binding so hydrogen bonding and hydrophobic interactions are responisble for binding. I have experimental data from ITC of binding free energy. I am wondering whether application of Umbrella Sampling would be a good aplication. I would like to put e.g. 10 ligands around my protein (200 residues) and see which of them went into my structure deep (stronger interaction) and then using position restrained dyunamics of my protein and other ligands pull crucial ligand and perform windows for Umbrella Sampling then obtaining free energy? The second thing I would like calculate is binding free energy of the second layer of ligands - I mean: they do aggregate one on the another, so in this case will Umbrella Sampling can be used to pull ligand from the another which stacked to my protein (posre of my protein and 1other ligands)? The third thing I am interested is chemical potential of my ligand in this system. Can you please suggest some technique to obtain it - further reading, tutorials? Thank you in advance, Steven -- 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
Antw: [gmx-users] Coarse-graining and cut-offs
Hi Thomas, Wouldn't it be an idea to smooth this tabulated potential within some range down to zero (1.0-1.4). One could use a simple single-exponential decay in a switch-function manner. Just one suggestion and maybe not your solution. Bests, Emanuel Thomas Schlesier schl...@uni-mainz.de 13.01.12 14.29 Uhr Dear all, first of all, sorry to this rather conceptional question, which is not totally to GROMOACS related. But probably anyone of you can help. In my simulations I use mesitylene as a solvent. In future i want to coarse-grain the full atomic mesitylene to an effective one-particle. For this i did a NPT-simulation to obtain the RDF (with regard to the COM of the molecules) from which i want to calculate an effective interaction potential by iterative boltzmann. The full-atomistic simulations (slovate + solvent) employed a cut-off of 1.4 nm. At this distance (1.4 nm) the RDF shows it second minimum (RDF=0.97) and after 1.8 nm the RDF is around 1.0 +/- 0.15 (I got the RDF only up to a distance of 2.3 nm). Now my question is how long should be the table for the effective potential (i.e. maximum distance for an interaction)? If i would use 1.4 nm, i would have a jump in the interaction potential (which is normal due to the truncation of the cut-off). But for coulomb-interaction one would have PME or other stuff which would correct the artifects to some degree. Or would it be better to use a long interaction table (interactions at longer distances) and truncate the table at a distance after 1.4 nm where the RDF is equal to 1? Hope anybody can give some insight. Greetings Thomas -- 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 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] About spacing in umbrella sampling
Dear justin, Thanks for your previous reply which one is reliable to get desired spacing in umbrella sampling either from output of g_dist or from pullx.xvg? If i choose spacing from pullx.xvg will it affect the result ? (poor sampling and poor free energy calculation). Thanks in Advance-- 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
Re: [gmx-users] About spacing in umbrella sampling
vidhya sankar wrote: Dear justin, Thanks for your previous reply which one is reliable to get desired spacing in umbrella sampling either from output of g_dist or from pullx.xvg? They should be equivalent. If i choose spacing from pullx.xvg will it affect the result ? (poor sampling and poor free energy calculation). The only way you get a poor result is if you have insufficient overlap or poor sampling of the configurations in each window. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] average force on solute
Hi, I am simulating a peptide in a box of water in gromacs 4.5.4 . From the trajectory, I want to compute the time-averaged force acting on the peptide. I found g_traj tool can provide information on force upon supplying the traj.trr file and g_traj help menu also suggests that using -af option one can get the average force on a selected group. But, I found a problem in executing the g_traj tool to calculate the average force. I find that if the .trr file do not store any coordinate ( but store only force), then the -af option actually do not work. Since I was interested in force, in my mdp output file option,I used following settings i.e in the .trr file I only write the force. Output frequency for coords (x), velocities (v) and forces (f) nstxout = 0 nstvout = 0 nstfout = 5 ; Output frequency for energies to log file and energy file nstlog = 5 nstcalcenergy = -1 nstenergy = 5000 ; Output frequency and precision for .xtc file nstxtcout = 1000 xtc_precision = 1000 But, after running the simulation, if I try to use g_traj to extract the force,using following command: g_traj_44 -f traj.trr -s -n -af -cf I get following warning and no average force is being written: WARNING: No coordinate frames found for option -cv or -cf No frames found for average force, will not write force.pdb I wonder, why one need to have coordinate stored as well to get the average force file or there is any other work-around for this or do I really need to also store coordinates in the trr file for getting the average force. If there is any other alternatives for getting the average force, please let me know. Thanks Sanku-- 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
