# \#gmx-sasa **URL:** https://gromacs.bioexcel.eu/tag/gmx-sasa/57.md [Latest](https://gromacs.bioexcel.eu/latest.md) · [Categories](https://gromacs.bioexcel.eu/categories.md) · [Tags](https://gromacs.bioexcel.eu/tags.md) --- ## [Having issue with gmx SASA giving values of 0 for specific protein](https://gromacs.bioexcel.eu/t/having-issue-with-gmx-sasa-giving-values-of-0-for-specific-protein/13709)
**Author:** [@dwat223](https://gromacs.bioexcel.eu/u/dwat223)\ **Replies:** 0\ **Last updated:** [September 8, 2026, 12:08am UTC](https://gromacs.bioexcel.eu/t/having-issue-with-gmx-sasa-giving-values-of-0-for-specific-protein/13709 "2026-09-08T00:08:31Z")
GROMACS version: 2025.2-foss-2023a-cuda-12.5.0-hybrid GROMACS modification: No Hi, I’m doing some work and it was suggested that I use gmx sasa to calculate the SASA of some binidng sites. I’m having issue with on part… --- ## [SASA Calculation](https://gromacs.bioexcel.eu/t/sasa-calculation/13311)
**Author:** [@zeshan07](https://gromacs.bioexcel.eu/u/zeshan07)\ **Replies:** 0\ **Last updated:** [March 18, 2026, 10:37am UTC](https://gromacs.bioexcel.eu/t/sasa-calculation/13311 "2026-03-18T10:37:51Z")
I have changed my probe from 0.14 to 0.186, but surprisingly the sasa have increased by a significant amount. What could be the possible reason? --- ## [Gromacs sasa for CG models](https://gromacs.bioexcel.eu/t/gromacs-sasa-for-cg-models/11691)
**Author:** [@Kenni3327](https://gromacs.bioexcel.eu/u/Kenni3327)\ **Replies:** 0\ **Last updated:** [March 6, 2025, 1:31pm UTC](https://gromacs.bioexcel.eu/t/gromacs-sasa-for-cg-models/11691 "2025-03-06T13:31:58Z")
GROMACS version:gromacs-2023 GROMACS modification: No Hi, I’m using gmx sasa to calculate the surface area for my martini models. I read the document and also checked the tutorial. I am still not clear about the format… --- ## [Gmx sasa for single atom in protein](https://gromacs.bioexcel.eu/t/gmx-sasa-for-single-atom-in-protein/11592)
**Author:** [@ghostpipierfish](https://gromacs.bioexcel.eu/u/ghostpipierfish)\ **Replies:** 0\ **Last updated:** [February 19, 2025, 12:48pm UTC](https://gromacs.bioexcel.eu/t/gmx-sasa-for-single-atom-in-protein/11592 "2025-02-19T12:48:22Z")
GROMACS version: 2019.3 GROMACS modification: No Hi, I’m trying to calculate the sasa of a single atom in my protein from a trajectory of the protein. Here is my command: gmx sasa -f md\_0\_1.xtc -s md\_0\_1.tpr -n index… --- ## [Identify solvent-exposed salt bridges](https://gromacs.bioexcel.eu/t/identify-solvent-exposed-salt-bridges/9214)
**Author:** [@Azam](https://gromacs.bioexcel.eu/u/Azam)\ **Replies:** 0\ **Last updated:** [May 24, 2024, 11:15am UTC](https://gromacs.bioexcel.eu/t/identify-solvent-exposed-salt-bridges/9214 "2024-05-24T11:15:53Z")
GROMACS version:2022 GROMACS modification: Yes/No how do identify solvent-exposed salt bridges of protein in solvent regarding each amino acid? please guide me . --- ## [Does SASA depend on the size of residue?](https://gromacs.bioexcel.eu/t/does-sasa-depend-on-the-size-of-residue/8768)
**Author:** [@ram.3](https://gromacs.bioexcel.eu/u/ram.3)\ **Replies:** 0\ **Last updated:** [April 2, 2024, 11:17am UTC](https://gromacs.bioexcel.eu/t/does-sasa-depend-on-the-size-of-residue/8768 "2024-04-02T11:17:50Z")
GROMACS version: 2021.4 GROMACS modification: No Hi everyone, I’m currently analyzing my dye-water simulations for SASA using gmx SASA. I have two dye residues of different sizes. I noticed that the smaller residue ha… --- ## [Do we need to process trajectory before sasa calculations?](https://gromacs.bioexcel.eu/t/do-we-need-to-process-trajectory-before-sasa-calculations/7896)
**Author:** [@Ema2022](https://gromacs.bioexcel.eu/u/Ema2022)\ **Replies:** 5\ **Last updated:** [January 16, 2024, 11:29am UTC](https://gromacs.bioexcel.eu/t/do-we-need-to-process-trajectory-before-sasa-calculations/7896 "2024-01-16T11:29:32Z")
Dear All, I would like to know whether we need to use gmx trjconv -pbc nojump and get processed trajectory to be used in gmx sasa calculations OR can we use the trajectory straightway from the MD, without processing it … --- ## [Hydrophobic SASA for a surface](https://gromacs.bioexcel.eu/t/hydrophobic-sasa-for-a-surface/6104)
**Author:** [@SerenaGiberti](https://gromacs.bioexcel.eu/u/SerenaGiberti)\ **Replies:** 0\ **Last updated:** [April 4, 2023, 8:55am UTC](https://gromacs.bioexcel.eu/t/hydrophobic-sasa-for-a-surface/6104 "2023-04-04T08:55:40Z")
Hi, I’m trying to get SASA information from a gold surface covered with ligands MD simulation. With gmx sasa i can only get the total SASA but I want the hydrophobic one. What should I do? Thanks Serena --- ## [Gmx sasa query](https://gromacs.bioexcel.eu/t/gmx-sasa-query/5892)
**Author:** [@DeekshaDewangan](https://gromacs.bioexcel.eu/u/DeekshaDewangan)\ **Replies:** 1\ **Last updated:** [March 10, 2023, 8:42am UTC](https://gromacs.bioexcel.eu/t/gmx-sasa-query/5892 "2023-03-10T08:42:04Z")
GROMACS version:5.1.2 GROMACS modification: Yes/No Here post your question After using command gmx sasa -s prod.tpr -f prod.xtc -or prod\_residue.xvg -o prod.xvg we are getting sasa of only 9 residues but in our prote… --- ## [SASA polar/non-polar calculation](https://gromacs.bioexcel.eu/t/sasa-polar-non-polar-calculation/5872)
**Author:** [@wintermute](https://gromacs.bioexcel.eu/u/wintermute)\ **Replies:** 0\ **Last updated:** [February 25, 2023, 11:15am UTC](https://gromacs.bioexcel.eu/t/sasa-polar-non-polar-calculation/5872 "2023-02-25T11:15:14Z")
GROMACS version: 2019.3 GROMACS modification: No Here post your question Hi there, I know Gromacs has a command gmx sasa but is there a command that can calculate polar/non-polar SASA? Or is there any other tool/pyt… --- ## [SASA per residue](https://gromacs.bioexcel.eu/t/sasa-per-residue/5768)
**Author:** [@ecemgungor](https://gromacs.bioexcel.eu/u/ecemgungor)\ **Replies:** 1\ **Last updated:** [February 9, 2023, 4:29pm UTC](https://gromacs.bioexcel.eu/t/sasa-per-residue/5768 "2023-02-09T16:29:55Z")
GROMACS version: version 2020.1-Ubuntu-2020.1-1 GROMACS modification: No Hello, I have a protein and I would like to calculate the SASA of the specific residues of my protein. In other words, I would like to perform S… --- ## [Optimising gmx sasa command](https://gromacs.bioexcel.eu/t/optimising-gmx-sasa-command/5425)
**Author:** [@arcyeus](https://gromacs.bioexcel.eu/u/arcyeus)\ **Replies:** 0\ **Last updated:** [December 13, 2022, 1:54am UTC](https://gromacs.bioexcel.eu/t/optimising-gmx-sasa-command/5425 "2022-12-13T01:54:33Z")
GROMACS version: 2022.4 GROMACS modification: Yes/No CUDA Here post your question I’m running a model with E. coli ATP synthase F0 as the protein embedded in a POPC bilayer. Currently, I’m using this command gmx sas… --- ## [SASA values different for full protein and sum of per residuewise SASA](https://gromacs.bioexcel.eu/t/sasa-values-different-for-full-protein-and-sum-of-per-residuewise-sasa/3124)
**Author:** [@Krushna](https://gromacs.bioexcel.eu/u/Krushna)\ **Replies:** 7\ **Last updated:** [November 17, 2021, 11:41am UTC](https://gromacs.bioexcel.eu/t/sasa-values-different-for-full-protein-and-sum-of-per-residuewise-sasa/3124 "2021-11-17T11:41:54Z")
GROMACS version: 5.0.7 GROMACS modification: No Hi all, I am analysing my protein-in-water type simulations for SASA (using gmx SASA). I wanted to compute the SASA values for each conformation. I was comparing for a c… --- ## [Calculate the solvation free energy](https://gromacs.bioexcel.eu/t/calculate-the-solvation-free-energy/3157)
**Author:** [@tahereh](https://gromacs.bioexcel.eu/u/tahereh)\ **Replies:** 1\ **Last updated:** [November 17, 2021, 10:36am UTC](https://gromacs.bioexcel.eu/t/calculate-the-solvation-free-energy/3157 "2021-11-17T10:36:39Z")
GROMACS version: GROMACS modification: Yes/No I calculated the solvation free energy using the gmx sasa code, and I know that this code estimates these energies from per-atom solvation energies per exposed surface area… --- ## [What Prob size is better for gmx SASA?](https://gromacs.bioexcel.eu/t/what-prob-size-is-better-for-gmx-sasa/2340)
**Author:** [@mj.rezayani](https://gromacs.bioexcel.eu/u/mj.rezayani)\ **Replies:** 1\ **Last updated:** [June 10, 2021, 1:24pm UTC](https://gromacs.bioexcel.eu/t/what-prob-size-is-better-for-gmx-sasa/2340 "2021-06-10T13:24:43Z")
Dear all, I want to calculate solvent accessible surface area using gmx sasa. The probe size is 0.14 nm by default. Do I have to change probe size to 0.315 ( sigma of Tip3p Oxygen)? When I changed it to 0.315 the avera… --- ## [Gmx sasa argument to output per-frame data?](https://gromacs.bioexcel.eu/t/gmx-sasa-argument-to-output-per-frame-data/653)
**Author:** [@denny](https://gromacs.bioexcel.eu/u/denny)\ **Replies:** 2\ **Last updated:** [August 12, 2020, 7:34pm UTC](https://gromacs.bioexcel.eu/t/gmx-sasa-argument-to-output-per-frame-data/653 "2020-08-12T19:34:36Z")
GROMACS version:2020.3 GROMACS modification: Yes/No I would like to output per-residue or per-atom sasa information every frame (or every 10th frame, etc). Am I correct that there is no such argument? To be clear I d…